1. oligo
  2. DESCRIPTION
Browse code

fixing vignette errors on linux

Benilton Carvalho authored on 08/03/2025 20:38:43
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DESCRIPTION
History View file @ e073acb
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.71.5
2 
+Version: 1.71.7
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Fixed: c-level changes, zlib, ::: imports, compilation flags

Benilton Carvalho authored on 06/03/2025 03:18:14
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DESCRIPTION
History View file @ d1e926a
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.71.2
2 
+Version: 1.71.5
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
... ... 
@@ -20,7 +20,8 @@ Imports: affyio (>= 1.35.0),
20 20 
          splines,
21 21 
          stats,
22 22 
          stats4,
23 
-         utils
23 
+         utils,
24 
+         bit
24 25 
 Enhances: doMC,
25 26 
           doMPI
26 27 
 LinkingTo: preprocessCore
Browse code

Update DESCRIPTION

remove zlibbioc

Benilton Carvalho authored on 05/03/2025 02:49:22 • GitHub committed on 05/03/2025 02:49:22
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DESCRIPTION
History View file @ cbab17c
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.71.1
2 
+Version: 1.71.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
... ... 
@@ -20,8 +20,7 @@ Imports: affyio (>= 1.35.0),
20 20 
          splines,
21 21 
          stats,
22 22 
          stats4,
23 
-         utils,
24 
-         zlibbioc
23 
+         utils
25 24 
 Enhances: doMC,
26 25 
           doMPI
27 26 
 LinkingTo: preprocessCore
Browse code

fixing C-level functions

Benilton Carvalho authored on 04/03/2025 14:16:23
Showing 1 changed files
DESCRIPTION
History View file @ 953b317
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.71.0
2 
+Version: 1.71.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 13:24:49
Showing 1 changed files
DESCRIPTION
History View file @ b720ab9
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.70.0
2 
+Version: 1.71.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 13:24:49
Showing 1 changed files
DESCRIPTION
History View file @ ce78773
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.69.2
2 
+Version: 1.70.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

fixing -Wunused-result warning

Benilton Carvalho authored on 04/06/2024 01:28:52
Showing 1 changed files
DESCRIPTION
History View file @ 73ec34d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.69.1
2 
+Version: 1.69.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

adding fixes to zlib calls

Benilton Carvalho authored on 03/06/2024 16:56:57
Showing 0 changed files
Browse code

fixing zlib probs

Benilton Carvalho authored on 02/06/2024 02:00:09
Showing 1 changed files
DESCRIPTION
History View file @ 30fb2b6
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.68.0
2 
+Version: 1.68.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
... ... 
@@ -79,5 +79,6 @@ Collate: AllGenerics.R
79 79 
          methods-PLMset.R
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          zzz.R
81 81 
 LazyLoad: Yes
82 
+URL: https://github.com/benilton/oligo
82 83 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
83 84 
         DifferentialExpression, ExonArray, GeneExpression, DataImport
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 14:14:15
Showing 1 changed files
DESCRIPTION
History View file @ 87cd053
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.68.0
2 
+Version: 1.69.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 14:14:15
Showing 1 changed files
DESCRIPTION
History View file @ f9b9ea0
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.67.0
2 
+Version: 1.68.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 13:35:20
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DESCRIPTION
History View file @ d97713f
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.66.0
2 
+Version: 1.67.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 13:35:20
Showing 1 changed files
DESCRIPTION
History View file @ e6e7283
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.65.0
2 
+Version: 1.66.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 13:42:11
Showing 1 changed files
DESCRIPTION
History View file @ 261cd56
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.64.0
2 
+Version: 1.65.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 13:42:11
Showing 1 changed files
DESCRIPTION
History View file @ e090605
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.63.0
2 
+Version: 1.64.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 14:39:32
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DESCRIPTION
History View file @ 3798b04
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.62.0
2 
+Version: 1.63.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 14:39:32
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DESCRIPTION
History View file @ 2ee0e0e
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.61.0
2 
+Version: 1.62.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 14:57:15
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DESCRIPTION
History View file @ d4b4e9e
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.60.0
2 
+Version: 1.61.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 14:57:15
Showing 1 changed files
DESCRIPTION
History View file @ d667332
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.59.0
2 
+Version: 1.60.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:48:16
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DESCRIPTION
History View file @ 7b3711c
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.58.0
2 
+Version: 1.59.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:48:16
Showing 1 changed files
DESCRIPTION
History View file @ 24a02c2
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.57.0
2 
+Version: 1.58.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:36:00
Showing 1 changed files
DESCRIPTION
History View file @ 000acca
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.56.0
2 
+Version: 1.57.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:36:00
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DESCRIPTION
History View file @ b3b6d7e
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.55.1
2 
+Version: 1.56.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Fixes on NAMESPACE: dbListFields no longer exported by RSQLite / Fixes on read.celfiles: argument verbose not being passed to smartCELreader

Benilton Carvalho authored on 03/11/2020 19:38:03
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DESCRIPTION
History View file @ 1124ae1
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.55.0
2 
+Version: 1.55.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:26:20
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DESCRIPTION
History View file @ 9d1e86d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.54.0
2 
+Version: 1.55.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:26:20
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DESCRIPTION
History View file @ 79534cb
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.53.2
2 
+Version: 1.54.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Small fix to DESCRIPTION which had duplicates in suggests, imports, depends, enhances.

Jim MacDonald authored on 10/08/2020 16:44:09
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DESCRIPTION
History View file @ b1a7e96
... ... 
@@ -22,8 +22,7 @@ Imports: affyio (>= 1.35.0),
22 22 
          stats4,
23 23 
          utils,
24 24 
          zlibbioc
25 
-Enhances: ff,
26 
-          doMC,
25 
+Enhances: doMC,
27 26 
           doMPI
28 27 
 LinkingTo: preprocessCore
29 28 
 Suggests: BSgenome.Hsapiens.UCSC.hg18,
... ... 
@@ -43,8 +42,6 @@ Suggests: BSgenome.Hsapiens.UCSC.hg18,
43 42 
           biomaRt,
44 43 
           AnnotationDbi,
45 44 
           ACME,
46 
-          biomaRt,
47 
-          AnnotationDbi,
48 45 
           RCurl
49 46 
 VignetteBuilder: knitr
50 47 
 Description: A package to analyze oligonucleotide arrays
Browse code

More updates to deal with breaking changes from ff. Also documented changes to oligoPLM class.

Jim MacDonald authored on 10/08/2020 16:10:11
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DESCRIPTION
History View file @ 91da409
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.53.0
2 
+Version: 1.53.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:11:38
Showing 1 changed files
DESCRIPTION
History View file @ c21a260
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.52.0
2 
+Version: 1.53.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:11:38
Showing 1 changed files
DESCRIPTION
History View file @ 14fee5c
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.51.2
2 
+Version: 1.52.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Removing dependency of GenomeGraphs - forgotten @ Rnw

Benilton Carvalho authored on 07/01/2020 21:51:19
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DESCRIPTION
History View file @ 4baedd7
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.51.1
2 
+Version: 1.51.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Updating version

Benilton Carvalho authored on 30/12/2019 06:00:52
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DESCRIPTION
History View file @ 16ab7f6
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.51.0
2 
+Version: 1.51.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Removing GenomeGraphs from dependency list

Benilton Carvalho authored on 30/12/2019 06:00:15
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DESCRIPTION
History View file @ 3f7d845
... ... 
@@ -42,12 +42,9 @@ Suggests: BSgenome.Hsapiens.UCSC.hg18,
42 42 
           RUnit,
43 43 
           biomaRt,
44 44 
           AnnotationDbi,
45 
-          GenomeGraphs,
46 
-          RCurl,
47 45 
           ACME,
48 46 
           biomaRt,
49 47 
           AnnotationDbi,
50 
-          GenomeGraphs,
51 48 
           RCurl
52 49 
 VignetteBuilder: knitr
53 50 
 Description: A package to analyze oligonucleotide arrays
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:34:39
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DESCRIPTION
History View file @ 9d376fa
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.50.0
2 
+Version: 1.51.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:07:34
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DESCRIPTION
History View file @ 9e5e8d4
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.49.0
2 
+Version: 1.50.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:10:39
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DESCRIPTION
History View file @ 6f67bdb
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.48.0
2 
+Version: 1.49.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:04
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DESCRIPTION
History View file @ f74a429
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.47.0
2 
+Version: 1.48.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:26
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DESCRIPTION
History View file @ f620294
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.46.0
2 
+Version: 1.47.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:42
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DESCRIPTION
History View file @ 42f2441
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.45.2
2 
+Version: 1.46.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

update from biocLite to BiocManager::install

LiNk-NY authored on 06/09/2018 22:33:07
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DESCRIPTION
History View file @ 9e179d5
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.45.1
2 
+Version: 1.45.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:53:22
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DESCRIPTION
History View file @ 787dc4a
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 Title: Preprocessing tools for oligonucleotide arrays
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:36
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-Version: 1.44.0
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5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
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bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:02
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 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
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bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:05
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-Version: 1.42.0
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+Version: 1.43.0
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
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bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:06
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-Version: 1.41.1
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+Version: 1.42.0
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Added error message in paMAS5 for PM-only arrays.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@131485 bc3139a8-67e5-0310-9ffc-ced21a209358

James MacDonald authored on 21/07/2017 17:30:23
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-Version: 1.41.0
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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 Package: oligo
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-Version: 1.40.0
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+Version: 1.41.0
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 Title: Preprocessing tools for oligonucleotide arrays
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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-Version: 1.39.1
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+Version: 1.40.0
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
Browse code

Adding Guido suggestions to PLM sets

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@128859 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/04/2017 19:09:17
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 Package: oligo
2 
-Version: 1.39.0
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+Version: 1.39.1
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
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-Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 
+Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles, Guido Hooiveld
6 6 
 Maintainer: Benilton Carvalho <benilton@unicamp.br>
7 7 
 Depends: R (>= 3.2.0),
8 8 
          BiocGenerics (>= 0.13.11),
Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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2 
-Version: 1.38.0
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+Version: 1.39.0
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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-Version: 1.37.2
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+Version: 1.38.0
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 Title: Preprocessing tools for oligonucleotide arrays
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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-Version: 1.37.1
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+Version: 1.37.2
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 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
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bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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-Version: 1.36.0
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+Version: 1.37.0
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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-Version: 1.35.2
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+Version: 1.36.0
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 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Fixing contact information

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@112283 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/01/2016 20:32:11
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@@ -1,9 +1,9 @@
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 Package: oligo
2 
-Version: 1.35.1
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+Version: 1.35.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
6 
-Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
6 
+Maintainer: Benilton Carvalho <benilton@unicamp.br>
7 7 
 Depends: R (>= 3.2.0),
8 8 
          BiocGenerics (>= 0.13.11),
9 9 
          oligoClasses (>= 1.29.6),
Browse code

Applying patch by Robert Castello to handle Glue Grant Affymetrix Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@112281 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/01/2016 20:28:12
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 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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-Version: 1.34.0
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+Version: 1.35.0
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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-Version: 1.33.1
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5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

testing git mirror

From: Benilton Carvalho <beniltoncarvalho@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@105789 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/07/2015 16:26:37
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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1 1 
 Package: oligo
2 
-Version: 1.31.13
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+Version: 1.32.0
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d774a8af561f824535fe7f00c7fd3a09122549f9

Fixing Suggests field to account for vignette dependencies



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102370 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/04/2015 03:50:03
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History View file @ 5b55aa1
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.31.12
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+Version: 1.31.13
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
... ... 
@@ -39,7 +39,16 @@ Suggests: BSgenome.Hsapiens.UCSC.hg18,
39 39 
           RColorBrewer,
40 40 
           oligoData,
41 41 
           BiocStyle, knitr,
42 
-          RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME
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+          RUnit,
43 
+          biomaRt,
44 
+          AnnotationDbi,
45 
+          GenomeGraphs,
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+          RCurl,
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+          ACME,
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+          biomaRt,
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+          AnnotationDbi,
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+          GenomeGraphs,
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+          RCurl
43 52 
 VignetteBuilder: knitr
44 53 
 Description: A package to analyze oligonucleotide arrays
45 54 
         (expression/SNP/tiling/exon) at probe-level. It currently
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ef010c284dcd2cbf5b7a37e6aa16ec003a916dde

Fixed syncing with annotation packages



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102368 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/04/2015 03:33:32
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2 
-Version: 1.31.11
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+Version: 1.31.12
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 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0c816a92bfdfb24bdeff0ee5044862216697a9da

Major vignette changes


Commit id: 1c53d01f00d360a07f21457615e170c6be85775f

Fixing vignette / copying pdf


Commit id: 1f9642271c5b44a5c6e6065dfb19e809c9c39ea5

Fixing vignette / copying pdf


Commit id: 57ef96b0cf8e272d1a1963e594e23ff7a1b1983a

Fixing vignette / copying pdf


Commit id: 5453d71fe6c13b605fc2efea247f705c9ae82021

Removing unused files


Commit id: 1fd34e14592678d81f44aa6041a611dec69ba52c

Fixing vignette / copying pdf


Commit id: 36be29a6b66d414ddde24f74ef1b79861527ffd2

Fixing vignette / copying pdf



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102332 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/04/2015 21:52:21
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@@ -39,7 +39,7 @@ Suggests: BSgenome.Hsapiens.UCSC.hg18,
39 39 
           RColorBrewer,
40 40 
           oligoData,
41 41 
           BiocStyle, knitr,
42 
-          RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl
42 
+          RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME
43 43 
 VignetteBuilder: knitr
44 44 
 Description: A package to analyze oligonucleotide arrays
45 45 
         (expression/SNP/tiling/exon) at probe-level. It currently
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6950924227f3428e6141d58848b16993aa8ffa3a

Still fixing the vignette and man pages


Commit id: 68e21935a8c5db58bfd0286760228dbeede6b033

Fixing vignette dependencies


Commit id: 3337652c826e3a19ee7f7a2c1dee3278a9942003

Merge branch 'master' of https://github.com/benilton/oligo

Fix by Nathaniel : package dependency


Commit id: 0843fee9e12778851b00af402bbd82c9f2111bcc

Fixing BUILD complaints: hidden file / Vignette error: citep -> cite


Commit id: 383972bb2216fb2a667c8a724d84d7a7dc49d5e2

Fixing BUILD complaints: hidden file



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102318 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/04/2015 06:25:50
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.31.9
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+Version: 1.31.11
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
... ... 
@@ -39,7 +39,7 @@ Suggests: BSgenome.Hsapiens.UCSC.hg18,
39 39 
           RColorBrewer,
40 40 
           oligoData,
41 41 
           BiocStyle, knitr,
42 
-          RUnit
42 
+          RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl
43 43 
 VignetteBuilder: knitr
44 44 
 Description: A package to analyze oligonucleotide arrays
45 45 
         (expression/SNP/tiling/exon) at probe-level. It currently
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: b705ee756b518a906deeb5e2096c4d1175d610f8

Merge pull request #26 from nhayden/master

add 'BSgenome.Hsapiens.UCSC.hg18' to Suggests

Commit id: e2b1df4186807ead39f00b84908483606db6aed0

add 'BSgenome.Hsapiens.UCSC.hg18' to Suggests



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102316 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/04/2015 03:01:41
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@@ -1,5 +1,5 @@
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-Version: 1.31.8
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+Version: 1.31.9
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 Title: Preprocessing tools for oligonucleotide arrays
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 Author: Benilton Carvalho and Rafael Irizarry
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 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
... ... 
@@ -26,7 +26,8 @@ Enhances: ff,
26 26 
           doMC,
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           doMPI
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 LinkingTo: preprocessCore
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-Suggests: hapmap100kxba,
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+Suggests: BSgenome.Hsapiens.UCSC.hg18,
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+          hapmap100kxba,
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           pd.hg.u95av2,
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           pd.mapping50k.xba240,
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           pd.huex.1.0.st.v2,
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2e4dbf584cda3fd2b9c4c6594778cd2eeb96cd0f

Fixing vignette



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102225 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/04/2015 20:39:45
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.31.7
2 
+Version: 1.31.8
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

add pd.hg.u95av2 to Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102128 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 08/04/2015 22:00:23
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@@ -27,6 +27,7 @@ Enhances: ff,
27 27 
           doMPI
28 28 
 LinkingTo: preprocessCore
29 29 
 Suggests: hapmap100kxba,
30 
+          pd.hg.u95av2,
30 31 
           pd.mapping50k.xba240,
31 32 
           pd.huex.1.0.st.v2,
32 33 
           pd.hg18.60mer.expr,
Browse code

bump version number

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102126 bc3139a8-67e5-0310-9ffc-ced21a209358

Nathaniel Hayden authored on 08/04/2015 21:30:29
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1 1 
 Package: oligo
2 
-Version: 1.31.6
2 
+Version: 1.31.7
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: e1746b944022acd32209f0f4a712715012e178b5

Fixing geenric for normalize (i.e., removing it) / Adding Travis-CI



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102074 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/04/2015 05:55:17
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.31.5
2 
+Version: 1.31.6
3 3 
 Title: Preprocessing tools for oligonucleotide arrays
4 4 
 Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 08614b78cd63768d99e8f013c09c4fe76cdd88f3

Removed defunct functions / added GenericArray / major vignette update



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@102006 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/04/2015 03:48:26
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1 1 
 Package: oligo
2 
-Version: 1.31.2
3 
-Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho and Rafael Irizarry.
2 
+Version: 1.31.5
3 
+Title: Preprocessing tools for oligonucleotide arrays
4 
+Author: Benilton Carvalho and Rafael Irizarry
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
6 6 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
7 
-Depends: R (>= 2.15.0),
8 
-         BiocGenerics (>= 0.3.2),
9 
-         oligoClasses (>= 1.25.4),
10 
-         Biobase (>= 2.17.8),
11 
-         Biostrings (>= 2.25.12)
12 
-Imports: affyio (>= 1.25.0),
13 
-         affxparser (>= 1.29.11),
14 
-         BiocGenerics (>= 0.3.2),
15 
-         DBI (>= 0.2-5),
7 
+Depends: R (>= 3.2.0),
8 
+         BiocGenerics (>= 0.13.11),
9 
+         oligoClasses (>= 1.29.6),
10 
+         Biobase (>= 2.27.3),
11 
+         Biostrings (>= 2.35.12)
12 
+Imports: affyio (>= 1.35.0),
13 
+         affxparser (>= 1.39.4),
14 
+         DBI (>= 0.3.1),
16 15 
          ff,
17 16 
          graphics,
18 17 
          methods,
19 
-         preprocessCore (>= 1.19.0),
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+         preprocessCore (>= 1.29.0),
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+         RSQLite (>= 1.0.0),
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          splines,
21 21 
          stats,
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          stats4,
... ... 
@@ -36,7 +36,9 @@ Suggests: hapmap100kxba,
36 36 
           limma,
37 37 
           RColorBrewer,
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           oligoData,
39 
+          BiocStyle, knitr,
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           RUnit
41 
+VignetteBuilder: knitr
40 42 
 Description: A package to analyze oligonucleotide arrays
41 43 
         (expression/SNP/tiling/exon) at probe-level. It currently
42 44 
         supports Affymetrix (CEL files) and NimbleGen arrays (XYS
Browse code

Fix "doi links in CITATION files.

The value of "doi" links should not be an absolute url, but one that looks like this:
10.1186/1471-2105-5-203



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@99157 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 06/02/2015 22:40:15
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.31.1
2 
+Version: 1.31.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry.
5 5 
 Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 62edd40c2ddfaeab0184edc4dfffe3e21e4735a8

bugfix: fixed class name

Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2015-01-11 04:07:54 -0200
Author date: 2015-01-11 04:07:54 -0200


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@98239 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/01/2015 06:08:08
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DESCRIPTION
History View file @ f560126
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@@ -11,7 +11,7 @@ Depends: R (>= 2.15.0),
11 11 
          Biostrings (>= 2.25.12)
12 12 
 Imports: affyio (>= 1.25.0),
13 13 
          affxparser (>= 1.29.11),
14 
-         BiocGenerics (>=0.3.2),
14 
+         BiocGenerics (>= 0.3.2),
15 15 
          DBI (>= 0.2-5),
16 16 
          ff,
17 17 
          graphics,
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: d24d79a7b5a2396cc35c17d61c80645e76e8fac2

adding support to generic arrays

Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2015-01-11 03:59:59 -0200
Author date: 2015-01-11 03:59:59 -0200


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@98236 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/01/2015 06:00:21
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DESCRIPTION
History View file @ baedfdd
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@@ -1,35 +1,76 @@
1 1 
 Package: oligo
2 
-Version: 1.31.0
2 
+Version: 1.31.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 
-        Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
6 
-        MacDonald, Matt Settles
4 
+Author: Benilton Carvalho and Rafael Irizarry.
5 
+Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
7 6 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
8 
-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>=
9 
-        1.25.4), Biobase (>= 2.17.8), Biostrings (>= 2.25.12)
10 
-Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), BiocGenerics (>=
11 
-        0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore
12 
-        (>= 1.19.0), splines, stats, stats4, utils, zlibbioc
13 
-Enhances: ff, doMC, doMPI
7 
+Depends: R (>= 2.15.0),
8 
+         BiocGenerics (>= 0.3.2),
9 
+         oligoClasses (>= 1.25.4),
10 
+         Biobase (>= 2.17.8),
11 
+         Biostrings (>= 2.25.12)
12 
+Imports: affyio (>= 1.25.0),
13 
+         affxparser (>= 1.29.11),
14 
+         BiocGenerics (>=0.3.2),
15 
+         DBI (>= 0.2-5),
16 
+         ff,
17 
+         graphics,
18 
+         methods,
19 
+         preprocessCore (>= 1.19.0),
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+         splines,
21 
+         stats,
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+         stats4,
23 
+         utils,
24 
+         zlibbioc
25 
+Enhances: ff,
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+          doMC,
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+          doMPI
14 28 
 LinkingTo: preprocessCore
15 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2,
16 
-        pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex,
17 
-        genefilter, limma, RColorBrewer, oligoData, RUnit
29 
+Suggests: hapmap100kxba,
30 
+          pd.mapping50k.xba240,
31 
+          pd.huex.1.0.st.v2,
32 
+          pd.hg18.60mer.expr,
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+          pd.hugene.1.0.st.v1,
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+          maqcExpression4plex,
35 
+          genefilter,
36 
+          limma,
37 
+          RColorBrewer,
38 
+          oligoData,
39 
+          RUnit
18 40 
 Description: A package to analyze oligonucleotide arrays
19 41 
         (expression/SNP/tiling/exon) at probe-level. It currently
20 42 
         supports Affymetrix (CEL files) and NimbleGen arrays (XYS
21 43 
         files).
22 44 
 License: LGPL (>= 2)
23 
-Collate: AllGenerics.R methods-GeneFeatureSet.R
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-        methods-ExonFeatureSet.R methods-ExpressionFeatureSet.R
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-        methods-ExpressionSet.R methods-LDS.R methods-FeatureSet.R
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-        methods-SnpFeatureSet.R methods-SnpCnvFeatureSet.R
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-        methods-TilingFeatureSet.R methods-HtaFeatureSet.R
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-        methods-DBPDInfo.R methods-background.R methods-normalization.R
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-        methods-summarization.R read.celfiles.R read.xysfiles.R
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-        utils-general.R utils-selectors.R todo-snp.R functions-crlmm.R
31 
-        functions-snprma.R justSNPRMA.R justCRLMM.R methods-snp6.R
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-        methods-genotype.R methods-PLMset.R zzz.R
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+Collate: AllGenerics.R
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+         methods-GenericArrays.R
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+         methods-GeneFeatureSet.R
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+         methods-ExonFeatureSet.R
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+         methods-ExpressionFeatureSet.R
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+         methods-ExpressionSet.R
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+         methods-LDS.R
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+         methods-FeatureSet.R
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+         methods-SnpFeatureSet.R
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+         methods-SnpCnvFeatureSet.R
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+         methods-TilingFeatureSet.R
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+         methods-HtaFeatureSet.R
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+         methods-DBPDInfo.R
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+         methods-background.R
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+         methods-normalization.R
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+         methods-summarization.R
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+         read.celfiles.R
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+         read.xysfiles.R
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+         utils-general.R
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+         utils-selectors.R
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+         todo-snp.R
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+         functions-crlmm.R
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+         functions-snprma.R
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+         justSNPRMA.R
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+         justCRLMM.R
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+         methods-snp6.R
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+         methods-genotype.R
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+         methods-PLMset.R
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+         zzz.R
33 74 
 LazyLoad: Yes
34 75 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
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         DifferentialExpression, ExonArray, GeneExpression, DataImport
Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
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1 1 
 Package: oligo
2 
-Version: 1.30.0
2 
+Version: 1.31.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
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 Package: oligo
2 
-Version: 1.29.1
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+Version: 1.30.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 20873e464ddef54558d5fdaf87d696594fa85dd1
Commit message: Fixing date issue triggered by files without date/time info in header
Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2014-05-13 08:18:02 -0300
Author date: 2014-05-13 08:18:02 -0300



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@90239 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/05/2014 11:18:12
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1 1 
 Package: oligo
2 
-Version: 1.29.0
2 
+Version: 1.29.1
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
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 Package: oligo
2 
-Version: 1.28.0
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+Version: 1.29.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.27.13
2 
+Version: 1.28.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 1cd41e04e6c9dff23a2650601301178db851b6c5
Commit message:
Committing forgotten change
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-03-10T15:13:01-03:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87257 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2014 18:13:08
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.27.12
2 
+Version: 1.27.13
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: 791d2a00b022d366083884fc80632c47516880db
Commit message:
Adding priority for sampleNames from phenoData to read.xysfiles
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-03-07T21:28:52-03:00

Commit id: 5c5007fbc165bc1b7dc397d60e98f18f178c6cda
Commit message:
Merge branch 'master' of https://github.com/benilton/oligo
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-03-07T21:29:02-03:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87222 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/03/2014 00:29:23
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.27.11
2 
+Version: 1.27.12
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 3e3f0576d4b57012d87f9e2da0363258faa16348
Commit message:
If phenoData is given, read.celfiles uses its sampleNames instead of using CEL filenames
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-03-07T21:04:49-03:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87218 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/03/2014 00:05:00
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.27.10
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+Version: 1.27.11
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 5 
         Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
Browse code

modify to new biocViews to DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87035 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 04/03/2014 22:12:21
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@@ -1,65 +1,35 @@
1 1 
 Package: oligo
2 
-Version: 1.27.9
2 
+Version: 1.27.10
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
4 
+Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
5 
+        Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
6 
+        MacDonald, Matt Settles
5 7 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
6 
-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.25.4),
7 
-         Biobase (>= 2.17.8), Biostrings (>= 2.25.12)
8 
-Imports: affyio (>= 1.25.0),
9 
-         affxparser (>= 1.29.11),
10 
-         BiocGenerics (>= 0.3.2),
11 
-         DBI (>= 0.2-5),
12 
-         ff,
13 
-         graphics,
14 
-         methods,
15 
-         preprocessCore (>= 1.19.0),
16 
-         splines,
17 
-         stats,
18 
-         stats4,
19 
-         utils,
20 
-         zlibbioc
8 
+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>=
9 
+        1.25.4), Biobase (>= 2.17.8), Biostrings (>= 2.25.12)
10 
+Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), BiocGenerics (>=
11 
+        0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore
12 
+        (>= 1.19.0), splines, stats, stats4, utils, zlibbioc
21 13 
 Enhances: ff, doMC, doMPI
22 14 
 LinkingTo: preprocessCore
23 
-Suggests: hapmap100kxba,
24 
-          pd.mapping50k.xba240,
25 
-          pd.huex.1.0.st.v2,
26 
-          pd.hg18.60mer.expr,
27 
-          pd.hugene.1.0.st.v1,
28 
-          maqcExpression4plex,
29 
-          genefilter,
30 
-          limma,
31 
-          RColorBrewer,
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-          oligoData,
33 
-          RUnit
34 
-Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
15 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2,
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+        pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex,
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+        genefilter, limma, RColorBrewer, oligoData, RUnit
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+Description: A package to analyze oligonucleotide arrays
19 
+        (expression/SNP/tiling/exon) at probe-level. It currently
20 
+        supports Affymetrix (CEL files) and NimbleGen arrays (XYS
21 
+        files).
35 22 
 License: LGPL (>= 2)
36 
-Collate: AllGenerics.R
37 
-         methods-GeneFeatureSet.R
38 
-         methods-ExonFeatureSet.R
39 
-         methods-ExpressionFeatureSet.R
40 
-         methods-ExpressionSet.R
41 
-         methods-LDS.R
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-         methods-FeatureSet.R
43 
-         methods-SnpFeatureSet.R
44 
-         methods-SnpCnvFeatureSet.R
45 
-         methods-TilingFeatureSet.R
46 
-         methods-HtaFeatureSet.R
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-         methods-DBPDInfo.R
48 
-         methods-background.R
49 
-         methods-normalization.R
50 
-         methods-summarization.R
51 
-         read.celfiles.R
52 
-         read.xysfiles.R
53 
-         utils-general.R
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-         utils-selectors.R
55 
-         todo-snp.R
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-         functions-crlmm.R
57 
-         functions-snprma.R
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-         justSNPRMA.R
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-         justCRLMM.R
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-         methods-snp6.R
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-         methods-genotype.R
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-         methods-PLMset.R
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-         zzz.R
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+Collate: AllGenerics.R methods-GeneFeatureSet.R
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+        methods-ExonFeatureSet.R methods-ExpressionFeatureSet.R
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+        methods-ExpressionSet.R methods-LDS.R methods-FeatureSet.R
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+        methods-SnpFeatureSet.R methods-SnpCnvFeatureSet.R
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+        methods-TilingFeatureSet.R methods-HtaFeatureSet.R
28 
+        methods-DBPDInfo.R methods-background.R methods-normalization.R
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+        methods-summarization.R read.celfiles.R read.xysfiles.R
30 
+        utils-general.R utils-selectors.R todo-snp.R functions-crlmm.R
31 
+        functions-snprma.R justSNPRMA.R justCRLMM.R methods-snp6.R
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+        methods-genotype.R methods-PLMset.R zzz.R
64 33 
 LazyLoad: Yes
65 
-biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, ExonArray, GeneExpression, Bioinformatics, DataImport
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+biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
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+        DifferentialExpression, ExonArray, GeneExpression, DataImport
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 5cbf940324ce067db7ca507ca2c05841b871f12e
Commit message:
Fixing summarization for HTA chips
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-18T18:05:01-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86569 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/02/2014 02:05:10
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1 1 
 Package: oligo
2 
-Version: 1.27.8
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+Version: 1.27.9
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 2d6c832e4de24d0b169948d71524ce58c106b3f3
Commit message:
Adding docs for rma() on HTA
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-12T18:23:37-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86399 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/02/2014 02:23:51
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1 1 
 Package: oligo
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-Version: 1.27.6
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+Version: 1.27.8
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 028a3dc9d2e78af05d2c9d7eb5467a059ad7a753
Commit message:
Getting unique probes for boxplot/hist
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-12T18:19:45-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86397 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/02/2014 02:20:04
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1 1 
 Package: oligo
2 
-Version: 1.27.4
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+Version: 1.27.6
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
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-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.25.3),
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+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.25.4),
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          Biobase (>= 2.17.8), Biostrings (>= 2.25.12)
8 8 
 Imports: affyio (>= 1.25.0),
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          affxparser (>= 1.29.11),
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: 5785d59bd0a3de48ba8e931c661bf54f4bf01840
Commit message:
Forgot to commit changes that defined classes needed for HTA data
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-10T10:40:08-08:00

Commit id: 9a3ea78a25ebb5996ad6674264ffe51926ab9ff4
Commit message:
Forgot to commit changes that defined classes needed for HTA data
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-10T13:08:27-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86286 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/02/2014 21:09:29
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 Package: oligo
2 
-Version: 1.27.3
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+Version: 1.27.4
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 6a022afefc0fe7fee50bc918c18d03a1390801a7
Commit message:
Draft support for HTA 2.0
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-08T11:54:04-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86235 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/02/2014 19:54:23
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 Package: oligo
2 
-Version: 1.27.2
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+Version: 1.27.3
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
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-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.21.18),
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+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.25.3),
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          Biobase (>= 2.17.8), Biostrings (>= 2.25.12)
8 8 
 Imports: affyio (>= 1.25.0),
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          affxparser (>= 1.29.11),
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: 3ccd121d5051f56ba99bf3deca36f3db1ec1409b
Commit message:
Fixing methods for HTA array
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-06T05:39:51-08:00

Commit id: ee617280bf31d5fb2031c46178eabf66382082ef
Commit message:
Merge branch 'master' of https://github.com/benilton/oligo
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-02-06T05:39:57-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86153 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/02/2014 13:40:18
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3 3 
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
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 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
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-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
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+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.21.18),
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          methods-SnpFeatureSet.R
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          methods-SnpCnvFeatureSet.R
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          methods-TilingFeatureSet.R
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+         methods-HtaFeatureSet.R
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          methods-DBPDInfo.R
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          methods-background.R
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          methods-normalization.R
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: 53932dcb4342ab6e817309ddcb5bf9ad923a9f9e
Commit message:
Adding code for HTA / fixing date-time insertion on protocolData
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-01-26T19:04:00-08:00

Commit id: 2effdf87bfd8ec7720b1c686e4d772be1c1a23eb
Commit message:
Merge branch 'master' of https://github.com/benilton/oligo
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-01-26T19:04:22-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@85828 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2014 03:04:57
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-Version: 1.27.1
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+Version: 1.27.2
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: f9032cf0520455968e577eb4c12b7352f7530b34
Commit message:
Moved Biostrings to Depends
Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
Commit date: 2014-01-24T05:48:10-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@85780 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/01/2014 13:49:11
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-Version: 1.27.0
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+Version: 1.27.1
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
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 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
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 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
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bump version after release branch has been created

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@81644 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:47:19
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

bump versions prior to creating BioC 2.13 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@81642 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:29:21
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
Browse code

merging bioc/github

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79114 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:33:20
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-Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Imports: affyio (>= 1.25.0),
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Removing dependency on RConverters.h - pointed by Prof Ripley

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79112 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:32:51
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bugfix: by M. Morgan - ParserGzXYS.c

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79111 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:32:35
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Removing dependency on RConverters.h - pointed by Prof Ripley

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79110 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:32:21
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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bump package versions after creating 2.11 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79109 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:32:07
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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Bump all packages before creating 2.11 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79108 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:31:53
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Browse code

Bugfix: by M. Morgan - ParserGzXYS.c

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79107 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:31:39
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Moving functions from .Deprecated to .Defunct

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79102 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:30:09
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Browse code

Fixed issue with annotation<- after generic was moved from Biobase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79101 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:29:47
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

The 'annotation' and 'annotation<-' generics have been moved from Biobase (2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these generics import them from BiocGenerics.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79100 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:29:29
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DESCRIPTION
History View file @ e4b13dc
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@@ -1,13 +1,14 @@
1 1 
 Package: oligo
2 
-Version: 1.21.6
2 
+Version: 1.21.7
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.15.0), oligoClasses (>= 1.19.41), Biobase (>= 2.17.7)
6 
+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
7 
+         Biobase (>= 2.17.8)
7 8 
 Imports: affyio (>= 1.25.0),
8 9 
          affxparser (>= 1.29.11),
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          Biostrings (>= 2.25.12),
10 
-         BiocGenerics (>= 0.3.1),
11 
+         BiocGenerics (>= 0.3.2),
11 12 
          DBI (>= 0.2-5),
12 13 
          ff,
13 14 
          graphics,
Browse code

Fixing docs and adding a script to get package versions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79099 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:29:12
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DESCRIPTION
History View file @ 4637b65
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@@ -1,18 +1,18 @@
1 1 
 Package: oligo
2 
-Version: 1.21.5
2 
+Version: 1.21.6
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35), Biobase (>= 2.15.4)
7 
-Imports: affyio (>= 1.23.2),
8 
-         affxparser (>= 1.27.5),
9 
-         Biostrings (>= 2.23.6),
10 
-         BiocGenerics (>= 0.1.14),
6 
+Depends: R (>= 2.15.0), oligoClasses (>= 1.19.41), Biobase (>= 2.17.7)
7 
+Imports: affyio (>= 1.25.0),
8 
+         affxparser (>= 1.29.11),
9 
+         Biostrings (>= 2.25.12),
10 
+         BiocGenerics (>= 0.3.1),
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          DBI (>= 0.2-5),
12 12 
          ff,
13 13 
          graphics,
14 14 
          methods,
15 
-         preprocessCore (>= 1.17.7),
15 
+         preprocessCore (>= 1.19.0),
16 16 
          splines,
17 17 
          stats,
18 18 
          stats4,
Browse code

Series of fixes regarding probe selection, including pmSeqeuence methods obeying target specification

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79098 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:28:57
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DESCRIPTION
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@@ -1,12 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 1.21.4
2 
+Version: 1.21.5
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35), Biobase (>= 2.15.4)
7 7 
 Imports: affyio (>= 1.23.2),
8 8 
          affxparser (>= 1.27.5),
9 
-         Biobase (>= 2.15.4),
10 9 
          Biostrings (>= 2.23.6),
11 10 
          BiocGenerics (>= 0.1.14),
12 11 
          DBI (>= 0.2-5),
Browse code

Bug fix: PA Calls didnt know about target

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79097 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:28:37
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History View file @ ee00e55
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.21.3
2 
+Version: 1.21.4
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Version fixing again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79096 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:28:21
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DESCRIPTION
History View file @ 111528e
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.20.3
2 
+Version: 1.21.3
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Version fixing

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79095 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:28:07
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History View file @ 7e81d77
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.21.3
2 
+Version: 1.20.3
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bumping version for pm<- mm<- transition

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79085 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:25:20
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DESCRIPTION
History View file @ 34e2d49
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.21.2
2 
+Version: 1.21.3
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Exporting exprs<- for users convenience

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79083 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:24:45
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History View file @ 8c55b4d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.21.1
2 
+Version: 1.21.2
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Merging with release: unifying vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79079 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:23:30
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1 1 
 Package: oligo
2 
-Version: 1.21.0
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+Version: 1.21.1
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

bumped version numbers after creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79076 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:22:24
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History View file @ fe9b2b7
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1 1 
 Package: oligo
2 
-Version: 1.20.0
2 
+Version: 1.21.0
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

first version bump prior to creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79075 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:22:09
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DESCRIPTION
History View file @ a554092
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.26
2 
+Version: 1.20.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

GitHub -> BioC svn

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79074 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:21:55
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1 1 
 Package: oligo
2 
-Version: 1.19.25
2 
+Version: 1.19.26
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Addressed issue in which probes without chr info would be removed from pmChr

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79073 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:21:35
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1 1 
 Package: oligo
2 
-Version: 1.19.24
2 
+Version: 1.19.25
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing probe subsetting

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79065 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:19:14
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1 1 
 Package: oligo
2 
-Version: 1.19.23
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+Version: 1.19.24
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixed selector

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79064 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:18:50
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1 1 
 Package: oligo
2 
-Version: 1.19.22
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+Version: 1.19.23
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

fixing Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79063 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:18:25
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History View file @ 2affa32
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@@ -22,7 +22,6 @@ Imports: affyio (>= 1.23.2),
22 22 
 Enhances: ff, doMC, doMPI
23 23 
 LinkingTo: preprocessCore
24 24 
 Suggests: hapmap100kxba,
25 
-          pd.hugene.1.0.st.v1,
26 25 
           pd.mapping50k.xba240,
27 26 
           pd.huex.1.0.st.v2,
28 27 
           pd.hg18.60mer.expr,
Browse code

fixing Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79062 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:18:10
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DESCRIPTION
History View file @ 26319fa
... ... 
@@ -26,6 +26,7 @@ Suggests: hapmap100kxba,
26 26 
           pd.mapping50k.xba240,
27 27 
           pd.huex.1.0.st.v2,
28 28 
           pd.hg18.60mer.expr,
29 
+          pd.hugene.1.0.st.v1,
29 30 
           maqcExpression4plex,
30 31 
           genefilter,
31 32 
           limma,
Browse code

added pd.hugene.1.0.st.v1 to suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79061 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:17:55
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History View file @ cf4971a
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.21
2 
+Version: 1.19.22
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
... ... 
@@ -22,6 +22,7 @@ Imports: affyio (>= 1.23.2),
22 22 
 Enhances: ff, doMC, doMPI
23 23 
 LinkingTo: preprocessCore
24 24 
 Suggests: hapmap100kxba,
25 
+          pd.hugene.1.0.st.v1,
25 26 
           pd.mapping50k.xba240,
26 27 
           pd.huex.1.0.st.v2,
27 28 
           pd.hg18.60mer.expr,
Browse code

Fixing PLM diags for Nimblegen

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79057 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:16:34
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History View file @ 80a6098
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.20
2 
+Version: 1.19.21
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Adding untracked files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79056 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:16:14
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History View file @ 06d8625
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1 1 
 Package: oligo
2 
-Version: 1.19.19
2 
+Version: 1.19.20
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing annoyances for R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79054 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:15:33
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History View file @ ba51a02
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@@ -3,7 +3,7 @@ Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
7 7 
 Imports: affyio (>= 1.23.2),
8 8 
          affxparser (>= 1.27.5),
9 9 
          Biobase (>= 2.15.4),
Browse code

Preparing docs for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79053 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:15:18
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DESCRIPTION
History View file @ be710d3
... ... 
@@ -3,7 +3,7 @@ Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
7 7 
 Imports: affyio (>= 1.23.2),
8 8 
          affxparser (>= 1.27.5),
9 9 
          Biobase (>= 2.15.4),
Browse code

Fixing annoyances for R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79052 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:15:03
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History View file @ 97211fc
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@@ -3,7 +3,7 @@ Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
7 7 
 Imports: affyio (>= 1.23.2),
8 8 
          affxparser (>= 1.27.5),
9 9 
          Biobase (>= 2.15.4),
Browse code

Preparing docs for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79051 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:14:43
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History View file @ d533fcc
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@@ -1,28 +1,25 @@
1 1 
 Package: oligo
2 
-Version: 1.19.18
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+Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0),
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-         oligoClasses (>= 1.13.9),
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-         foreach
9 
-Imports: affyio (>= 1.19.4),
10 
-         affxparser (>= 1.23.1),
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-         Biobase (>= 2.11.8),
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-         Biostrings,
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
7 
+Imports: affyio (>= 1.23.2),
8 
+         affxparser (>= 1.27.5),
9 
+         Biobase (>= 2.15.4),
10 
+         Biostrings (>= 2.23.6),
13 11 
          BiocGenerics (>= 0.1.14),
14 12 
          DBI (>= 0.2-5),
15 13 
          ff,
16 14 
          graphics,
17 15 
          methods,
18 
-         preprocessCore (>= 1.17.5),
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+         preprocessCore (>= 1.17.7),
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          splines,
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          stats,
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          stats4,
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          utils,
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          zlibbioc
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-Enhances: ff,
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-          snow
22 
+Enhances: ff, doMC, doMPI
26 23 
 LinkingTo: preprocessCore
27 24 
 Suggests: hapmap100kxba,
28 25 
           pd.mapping50k.xba240,
Browse code

Reverting DESCRIPTION to something that the BioC builder recognizes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79048 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:13:58
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DESCRIPTION
History View file @ c640312
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@@ -1,14 +1,7 @@
1 1 
 Package: oligo
2 
-Version: 1.19.17
2 
+Version: 1.19.18
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
-            person("Rafael", "Irizarry", role="aut"),
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-            person("Ben", "Bolstad", role="ctb"),
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-            person("Vincent", "Carey", role="ctb"),
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-            person("Robert", "Gentleman", role="ctb"),
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-            person("Wolfgang", "Huber", role="ctb"),
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-            person("Jim", "MacDonald", role="ctb"),
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-            person("Harris", "Jaffee", role="ctb"))
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+Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
12 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
13 6 
 Depends: R (>= 2.14.0),
14 7 
          oligoClasses (>= 1.13.9),
Browse code

add Maintainer field or BioC build system will skip package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79041 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:12:21
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DESCRIPTION
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@@ -9,6 +9,7 @@ Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilto
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             person("Wolfgang", "Huber", role="ctb"),
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             person("Jim", "MacDonald", role="ctb"),
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             person("Harris", "Jaffee", role="ctb"))
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+Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
12 13 
 Depends: R (>= 2.14.0),
13 14 
          oligoClasses (>= 1.13.9),
14 15 
          foreach
Browse code

minor fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79039 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:11:53
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DESCRIPTION
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1 1 
 Package: oligo
2 
-Version: 1.19.16
2 
+Version: 1.19.17
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

Merge branch 'cleanPLM'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79034 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:10:38
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1 1 
 Package: oligo
2 
-Version: 1.19.15
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+Version: 1.19.16
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

improving speed for fitProbeLevelModel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79029 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:09:26
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.14
2 
+Version: 1.19.15
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

Fixing imports from BiocGenerics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79027 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:08:55
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DESCRIPTION
History View file @ 776133c
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@@ -16,12 +16,12 @@ Imports: affyio (>= 1.19.4),
16 16 
          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
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-         BiocGenerics,
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+         BiocGenerics (>= 0.1.14),
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          DBI (>= 0.2-5),
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          ff,
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          graphics,
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          methods,
24 
-         preprocessCore (>= 1.13.5),
24 
+         preprocessCore (>= 1.17.5),
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          splines,
26 26 
          stats,
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          stats4,
Browse code

cleaning R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79026 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:08:40
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DESCRIPTION
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@@ -16,12 +16,12 @@ Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
19 
-         BiocGenerics (>= 0.1.14),
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+         BiocGenerics,
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          DBI (>= 0.2-5),
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          ff,
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          graphics,
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          methods,
24 
-         preprocessCore (>= 1.17.5),
24 
+         preprocessCore (>= 1.13.5),
25 25 
          splines,
26 26 
          stats,
27 27 
          stats4,
Browse code

Fixing imports from BiocGenerics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79019 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:07:00
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DESCRIPTION
History View file @ a8a9f5d
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@@ -16,12 +16,12 @@ Imports: affyio (>= 1.19.4),
16 16 
          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
19 
-         BiocGenerics,
19 
+         BiocGenerics (>= 0.1.14),
20 20 
          DBI (>= 0.2-5),
21 21 
          ff,
22 22 
          graphics,
23 23 
          methods,
24 
-         preprocessCore (>= 1.13.5),
24 
+         preprocessCore (>= 1.17.5),
25 25 
          splines,
26 26 
          stats,
27 27 
          stats4,
Browse code

cleaning R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79018 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:06:46
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DESCRIPTION
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@@ -16,12 +16,12 @@ Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
19 
-         BiocGenerics (>= 0.1.14),
19 
+         BiocGenerics,
20 20 
          DBI (>= 0.2-5),
21 21 
          ff,
22 22 
          graphics,
23 23 
          methods,
24 
-         preprocessCore (>= 1.17.5),
24 
+         preprocessCore (>= 1.13.5),
25 25 
          splines,
26 26 
          stats,
27 27 
          stats4,
Browse code

Fixing imports from BiocGenerics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79011 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:05:08
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DESCRIPTION
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@@ -1,23 +1,30 @@
1 1 
 Package: oligo
2 2 
 Version: 1.19.14
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 
-Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.13.0),
7 
-         BiocGenerics (>= 0.1.11),
4 
+Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
+            person("Rafael", "Irizarry", role="aut"),
6 
+            person("Ben", "Bolstad", role="ctb"),
7 
+            person("Vincent", "Carey", role="ctb"),
8 
+            person("Robert", "Gentleman", role="ctb"),
9 
+            person("Wolfgang", "Huber", role="ctb"),
10 
+            person("Jim", "MacDonald", role="ctb"),
11 
+            person("Harris", "Jaffee", role="ctb"))
12 
+Depends: R (>= 2.14.0),
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          oligoClasses (>= 1.13.9),
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          foreach
10 15 
 Imports: affyio (>= 1.19.4),
11 16 
          affxparser (>= 1.23.1),
12 17 
          Biobase (>= 2.11.8),
13 18 
          Biostrings,
19 
+         BiocGenerics (>= 0.1.14),
14 20 
          DBI (>= 0.2-5),
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          ff,
16 22 
          graphics,
17 23 
          methods,
18 
-         preprocessCore (>= 1.13.5),
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+         preprocessCore (>= 1.17.5),
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          splines,
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          stats,
27 
+         stats4,
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          utils,
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          zlibbioc
23 30 
 Enhances: ff,
Browse code

Import boxplot, image, and residuals generics from BiocGenerics.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79008 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:04:27
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DESCRIPTION
History View file @ 4805411
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@@ -1,22 +1,16 @@
1 1 
 Package: oligo
2 
-Version: 1.19.13
2 
+Version: 1.19.14
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
-            person("Rafael", "Irizarry", role="aut"),
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-            person("Ben", "Bolstad", role="ctb"),
7 
-            person("Vincent", "Carey", role="ctb"),
8 
-            person("Robert", "Gentleman", role="ctb"),
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-            person("Wolfgang", "Huber", role="ctb"),
10 
-            person("Jim", "MacDonald", role="ctb"),
11 
-            person("Harris", "Jaffee", role="ctb"))
12 
-Depends: R (>= 2.14.0),
4 
+Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 
+Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
+Depends: R (>= 2.13.0),
7 
+         BiocGenerics (>= 0.1.11),
13 8 
          oligoClasses (>= 1.13.9),
14 9 
          foreach
15 10 
 Imports: affyio (>= 1.19.4),
16 11 
          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
19 
-         BiocGenerics,
20 14 
          DBI (>= 0.2-5),
21 15 
          ff,
22 16 
          graphics,
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@@ -24,7 +18,6 @@ Imports: affyio (>= 1.19.4),
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          preprocessCore (>= 1.13.5),
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          splines,
26 20 
          stats,
27 
-         stats4,
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          utils,
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          zlibbioc
30 23 
 Enhances: ff,
Browse code

cleaning R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79007 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:04:12
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DESCRIPTION
History View file @ 56bbfbb
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@@ -1,15 +1,22 @@
1 1 
 Package: oligo
2 2 
 Version: 1.19.13
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 
-Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.13.0),
4 
+Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
+            person("Rafael", "Irizarry", role="aut"),
6 
+            person("Ben", "Bolstad", role="ctb"),
7 
+            person("Vincent", "Carey", role="ctb"),
8 
+            person("Robert", "Gentleman", role="ctb"),
9 
+            person("Wolfgang", "Huber", role="ctb"),
10 
+            person("Jim", "MacDonald", role="ctb"),
11 
+            person("Harris", "Jaffee", role="ctb"))
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+Depends: R (>= 2.14.0),
7 13 
          oligoClasses (>= 1.13.9),
8 14 
          foreach
9 15 
 Imports: affyio (>= 1.19.4),
10 16 
          affxparser (>= 1.23.1),
11 17 
          Biobase (>= 2.11.8),
12 18 
          Biostrings,
19 
+         BiocGenerics,
13 20 
          DBI (>= 0.2-5),
14 21 
          ff,
15 22 
          graphics,
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@@ -17,6 +24,7 @@ Imports: affyio (>= 1.19.4),
17 24 
          preprocessCore (>= 1.13.5),
18 25 
          splines,
19 26 
          stats,
27 
+         stats4,
20 28 
          utils,
21 29 
          zlibbioc
22 30 
 Enhances: ff,
Browse code

accid. committed wrong branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@79001 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:02:41
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.12-0
2 
+Version: 1.19.13
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

rewriting fitPLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78996 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:01:21
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DESCRIPTION
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@@ -4,7 +4,8 @@ Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
7 
-         oligoClasses (>= 1.13.9)
7 
+         oligoClasses (>= 1.13.9),
8 
+         foreach
8 9 
 Imports: affyio (>= 1.19.4),
9 10 
          affxparser (>= 1.23.1),
10 11 
          Biobase (>= 2.11.8),
Browse code

removing more affyPLM stuff

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78994 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:00:40
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DESCRIPTION
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@@ -58,7 +58,6 @@ Collate: AllGenerics.R
58 58 
          justCRLMM.R
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          methods-snp6.R
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          methods-genotype.R
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-         PLM_internal.R
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          methods-PLMset.R
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          zzz.R
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 LazyLoad: Yes
Browse code

Removed C code fom affyPLM / removed fitPLM / doing PLM through preprocessCore soon

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78993 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 19:00:22
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@@ -59,7 +59,6 @@ Collate: AllGenerics.R
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          methods-snp6.R
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          methods-genotype.R
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          PLM_internal.R
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-         fitPLM.R
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          methods-PLMset.R
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          zzz.R
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 LazyLoad: Yes
Browse code

tracking: removal of affyPLM C-code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78992 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:59:51
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.11
2 
+Version: 1.19.12-0
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

fix whitespace formatting problem

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78986 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:58:19
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.10
2 
+Version: 1.19.11
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Merging GitHub and BioC

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78985 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:58:02
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.9
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+Version: 1.19.10
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Now built with Makevars(.win) and make sure that it is not deleted by cleanup(.win). Makevars points to proper libraries, including zlibbioc's version of libz on windows.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78982 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:57:10
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.8
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+Version: 1.19.9
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Adding 1st unit test

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78981 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:56:45
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.7
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+Version: 1.19.8
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -29,7 +29,8 @@ Suggests: hapmap100kxba,
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           genefilter,
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           limma,
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           RColorBrewer,
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-          oligoData
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+          oligoData,
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+          RUnit
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 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
34 35 
 License: LGPL (>= 2)
35 36 
 Collate: AllGenerics.R
Browse code

removed _new_ getProbeIndex to get backwards compatibility

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78978 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:55:41
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
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-Version: 1.19.6
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+Version: 1.19.7
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Merged cleanup

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78975 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:55:12
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 Package: oligo
2 
-Version: 1.19.5-1
2 
+Version: 1.19.6
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
4 
+Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
7 7 
          oligoClasses (>= 1.13.9)
Browse code

Removed configure* src/Makecars*

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78974 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:54:58
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 Package: oligo
2 
-Version: 1.19.5
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+Version: 1.19.5-1
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Improved selector / added file to Collate

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78972 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:54:27
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 Package: oligo
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-Version: 1.19.4
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+Version: 1.19.5
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -49,6 +49,7 @@ Collate: AllGenerics.R
49 49 
          read.celfiles.R
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          read.xysfiles.R
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          utils-general.R
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+         utils-selectors.R
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          todo-snp.R
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          functions-crlmm.R
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          functions-snprma.R
Browse code

Improving implementation of selectors.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78970 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2013 18:53:53
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1 1 
 Package: oligo
2 
-Version: 1.25.2
2 
+Version: 1.19.4
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 
-Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
6 
-Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
7 
-         Biobase (>= 2.17.8)
8 
-Imports: affyio (>= 1.25.0),
9 
-         affxparser (>= 1.29.11),
10 
-         Biostrings (>= 2.25.12),
11 
-         BiocGenerics (>= 0.3.2),
4 
+Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 
+Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
+Depends: R (>= 2.13.0),
7 
+         oligoClasses (>= 1.13.9)
8 
+Imports: affyio (>= 1.19.4),
9 
+         affxparser (>= 1.23.1),
10 
+         Biobase (>= 2.11.8),
11 
+         Biostrings,
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          DBI (>= 0.2-5),
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          ff,
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          graphics,
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          methods,
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-         preprocessCore (>= 1.19.0),
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+         preprocessCore (>= 1.13.5),
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          splines,
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          stats,
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-         stats4,
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          utils,
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          zlibbioc
22 
-Enhances: ff, doMC, doMPI
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+Enhances: ff,
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+          snow
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba,
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           pd.mapping50k.xba240,
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           pd.huex.1.0.st.v2,
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           pd.hg18.60mer.expr,
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-          pd.hugene.1.0.st.v1,
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           maqcExpression4plex,
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           genefilter,
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           limma,
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           RColorBrewer,
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-          oligoData,
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-          RUnit
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+          oligoData
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 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
36 34 
 License: LGPL (>= 2)
37 35 
 Collate: AllGenerics.R
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@@ -51,7 +49,6 @@ Collate: AllGenerics.R
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          read.celfiles.R
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          read.xysfiles.R
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          utils-general.R
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-         utils-selectors.R
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          todo-snp.R
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          functions-crlmm.R
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          functions-snprma.R
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          justCRLMM.R
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          methods-snp6.R
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          methods-genotype.R
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+         PLM_internal.R
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+         fitPLM.R
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          methods-PLMset.R
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          zzz.R
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 LazyLoad: Yes
Browse code

BUG FIX: fixed order in which probes are read in justSNPRMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@78722 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/07/2013 20:53:15
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 Package: oligo
2 
-Version: 1.25.1
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+Version: 1.25.2
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 
-Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
5 
+Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
6 6 
 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
7 7 
          Biobase (>= 2.17.8)
8 8 
 Imports: affyio (>= 1.25.0),
Browse code

bumping version to sync with git

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@77041 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/05/2013 19:59:59
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 Package: oligo
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+Version: 1.25.1
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bump y in version x.y.z to odd number in devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@75270 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 22:06:11
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-Version: 1.24.0
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

bump y of x.y.z version number for BioC 2.12 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@75263 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 21:32:27
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 Package: oligo
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-Version: 1.23.1
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Removing dependency on RConverters.h - pointed by Prof Ripley

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@72253 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/01/2013 03:41:54
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 Package: oligo
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-Version: 1.21.10
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+Version: 1.23.1
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bugfix: by M. Morgan - ParserGzXYS.c

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@72252 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/01/2013 03:41:39
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

bump package versions after creating 2.11 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@70052 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:43:56
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bump all packages before creating 2.11 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@70050 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:16:24
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bugfix: by M. Morgan - ParserGzXYS.c

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@70047 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/10/2012 21:10:21
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Moving functions from .Deprecated to .Defunct

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@69904 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/09/2012 17:16:44
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixed issue with annotation<- after generic was moved from Biobase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@69891 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/09/2012 01:22:08
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

The 'annotation' and 'annotation<-' generics have been moved from Biobase (2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these generics import them from BiocGenerics.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@69535 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 18/09/2012 18:38:46
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 Package: oligo
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-Version: 1.21.6
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+Version: 1.21.7
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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-Depends: R (>= 2.15.0), oligoClasses (>= 1.19.41), Biobase (>= 2.17.7)
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+Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43),
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+         Biobase (>= 2.17.8)
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 Imports: affyio (>= 1.25.0),
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          affxparser (>= 1.29.11),
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          Biostrings (>= 2.25.12),
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-         BiocGenerics (>= 0.3.1),
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+         BiocGenerics (>= 0.3.2),
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          DBI (>= 0.2-5),
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          ff,
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          graphics,
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Merge branch 'master' of github.com:benilton/oligo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@69368 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/09/2012 11:09:00
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 Package: oligo
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-Version: 1.21.5
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+Version: 1.21.6
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35), Biobase (>= 2.15.4)
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-Imports: affyio (>= 1.23.2),
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-         affxparser (>= 1.27.5),
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-         Biostrings (>= 2.23.6),
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-         BiocGenerics (>= 0.1.14),
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+Depends: R (>= 2.15.0), oligoClasses (>= 1.19.41), Biobase (>= 2.17.7)
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+Imports: affyio (>= 1.25.0),
8 
+         affxparser (>= 1.29.11),
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+         Biostrings (>= 2.25.12),
10 
+         BiocGenerics (>= 0.3.1),
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          DBI (>= 0.2-5),
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          ff,
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          graphics,
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          methods,
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+         preprocessCore (>= 1.19.0),
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          splines,
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          stats,
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          stats4,
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Series of fixes regarding probe selection, including pmSeqeuence methods obeying target specification

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@67899 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/07/2012 23:29:18
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 Package: oligo
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-Version: 1.21.4
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
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+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35), Biobase (>= 2.15.4)
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 Imports: affyio (>= 1.23.2),
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Bug fix: PA Calls didnt know about target

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@67273 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/07/2012 14:59:17
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bugfix: target argument wasnt passed to normalize/backgroundCorrect

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@65262 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/04/2012 00:18:52
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Exporting exprs<- for users convenience

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@65236 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/04/2012 13:39:51
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

syncing stable-devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64894 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/04/2012 14:02:46
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 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

bumped version numbers after creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64680 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:15:56
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

first version bump prior to creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64678 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:05:02
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DESCRIPTION
History View file @ 8553e80
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.26
2 
+Version: 1.20.0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

GitHub -> BioC svn

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64660 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/03/2012 17:28:23
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1 1 
 Package: oligo
2 
-Version: 1.19.24
2 
+Version: 1.19.26
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing probe subsetting

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64398 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2012 13:56:00
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History View file @ 523cc07
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1 1 
 Package: oligo
2 
-Version: 1.19.23
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+Version: 1.19.24
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixed selector

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64396 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2012 03:51:05
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History View file @ 16dfbba
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.22
2 
+Version: 1.19.23
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

fixing Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64361 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/03/2012 19:46:10
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History View file @ 2e403fe
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@@ -22,7 +22,6 @@ Imports: affyio (>= 1.23.2),
22 22 
 Enhances: ff, doMC, doMPI
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba,
25 
-          pd.hugene.1.0.st.v1,
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           pd.mapping50k.xba240,
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           pd.huex.1.0.st.v2,
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           pd.hg18.60mer.expr,
Browse code

fixing Suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64360 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/03/2012 19:42:21
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DESCRIPTION
History View file @ 0303eed
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@@ -26,6 +26,7 @@ Suggests: hapmap100kxba,
26 26 
           pd.mapping50k.xba240,
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           pd.huex.1.0.st.v2,
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           pd.hg18.60mer.expr,
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+          pd.hugene.1.0.st.v1,
29 30 
           maqcExpression4plex,
30 31 
           genefilter,
31 32 
           limma,
Browse code

added pd.hugene.1.0.st.v1 to suggests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64358 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 23/03/2012 19:29:41
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History View file @ c4c36c0
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.21
2 
+Version: 1.19.22
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
... ... 
@@ -22,6 +22,7 @@ Imports: affyio (>= 1.23.2),
22 22 
 Enhances: ff, doMC, doMPI
23 23 
 LinkingTo: preprocessCore
24 24 
 Suggests: hapmap100kxba,
25 
+          pd.hugene.1.0.st.v1,
25 26 
           pd.mapping50k.xba240,
26 27 
           pd.huex.1.0.st.v2,
27 28 
           pd.hg18.60mer.expr,
Browse code

fixing vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64354 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/03/2012 18:48:20
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History View file @ 3d75006
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.20
2 
+Version: 1.19.21
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Adding untracked files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64301 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/03/2012 21:12:50
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History View file @ 1bf279f
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.19
2 
+Version: 1.19.20
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing annoyances for R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64275 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/03/2012 11:58:30
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History View file @ 3f64d1e
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@@ -3,7 +3,7 @@ Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35)
7 7 
 Imports: affyio (>= 1.23.2),
8 8 
          affxparser (>= 1.27.5),
9 9 
          Biobase (>= 2.15.4),
Browse code

Preparing docs for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@64274 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/03/2012 11:58:19
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History View file @ 07b41ab
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@@ -1,28 +1,25 @@
1 1 
 Package: oligo
2 
-Version: 1.19.18
2 
+Version: 1.19.19
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.14.0),
7 
-         oligoClasses (>= 1.13.9),
8 
-         foreach
9 
-Imports: affyio (>= 1.19.4),
10 
-         affxparser (>= 1.23.1),
11 
-         Biobase (>= 2.11.8),
12 
-         Biostrings,
6 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.13.9)
7 
+Imports: affyio (>= 1.23.2),
8 
+         affxparser (>= 1.27.5),
9 
+         Biobase (>= 2.15.4),
10 
+         Biostrings (>= 2.23.6),
13 11 
          BiocGenerics (>= 0.1.14),
14 12 
          DBI (>= 0.2-5),
15 13 
          ff,
16 14 
          graphics,
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          methods,
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-         preprocessCore (>= 1.17.5),
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+         preprocessCore (>= 1.17.7),
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          splines,
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          stats,
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          stats4,
22 20 
          utils,
23 21 
          zlibbioc
24 
-Enhances: ff,
25 
-          snow
22 
+Enhances: ff, doMC, doMPI
26 23 
 LinkingTo: preprocessCore
27 24 
 Suggests: hapmap100kxba,
28 25 
           pd.mapping50k.xba240,
Browse code

Reverting DESCRIPTION to something that the BioC builder recognizes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63946 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/03/2012 10:27:01
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DESCRIPTION
History View file @ cfe8104
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@@ -1,14 +1,7 @@
1 1 
 Package: oligo
2 
-Version: 1.19.17
2 
+Version: 1.19.18
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
-            person("Rafael", "Irizarry", role="aut"),
6 
-            person("Ben", "Bolstad", role="ctb"),
7 
-            person("Vincent", "Carey", role="ctb"),
8 
-            person("Robert", "Gentleman", role="ctb"),
9 
-            person("Wolfgang", "Huber", role="ctb"),
10 
-            person("Jim", "MacDonald", role="ctb"),
11 
-            person("Harris", "Jaffee", role="ctb"))
4 
+Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles
12 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
13 6 
 Depends: R (>= 2.14.0),
14 7 
          oligoClasses (>= 1.13.9),
Browse code

add Maintainer field or BioC build system will skip package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63828 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/03/2012 20:19:58
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DESCRIPTION
History View file @ ae1f4c6
... ... 
@@ -9,6 +9,7 @@ Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilto
9 9 
             person("Wolfgang", "Huber", role="ctb"),
10 10 
             person("Jim", "MacDonald", role="ctb"),
11 11 
             person("Harris", "Jaffee", role="ctb"))
12 
+Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
12 13 
 Depends: R (>= 2.14.0),
13 14 
          oligoClasses (>= 1.13.9),
14 15 
          foreach
Browse code

minor fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63793 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/03/2012 00:44:08
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History View file @ fee3259
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.16
2 
+Version: 1.19.17
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

Merge branch 'cleanPLM'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63742 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/03/2012 04:55:23
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.15
2 
+Version: 1.19.16
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

improving speed for fitProbeLevelModel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63737 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/03/2012 04:44:13
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History View file @ 3ae8d21
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.14
2 
+Version: 1.19.15
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 5 
             person("Rafael", "Irizarry", role="aut"),
Browse code

Fixing imports from BiocGenerics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63714 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2012 00:18:05
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History View file @ d8fc7d6
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@@ -16,12 +16,12 @@ Imports: affyio (>= 1.19.4),
16 16 
          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
18 18 
          Biostrings,
19 
-         BiocGenerics,
19 
+         BiocGenerics (>= 0.1.14),
20 20 
          DBI (>= 0.2-5),
21 21 
          ff,
22 22 
          graphics,
23 23 
          methods,
24 
-         preprocessCore (>= 1.13.5),
24 
+         preprocessCore (>= 1.17.5),
25 25 
          splines,
26 26 
          stats,
27 27 
          stats4,
Browse code

cleaning R CMD check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63713 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2012 00:17:55
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DESCRIPTION
History View file @ a560142
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@@ -1,16 +1,22 @@
1 1 
 Package: oligo
2 2 
 Version: 1.19.14
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 
-Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 
-Depends: R (>= 2.13.0),
7 
-         BiocGenerics (>= 0.1.11),
4 
+Authors@R: c(person("Benilton", "Carvalho", role=c("aut", "cre"), email="Benilton.Carvalho@cancer.org.uk"),
5 
+            person("Rafael", "Irizarry", role="aut"),
6 
+            person("Ben", "Bolstad", role="ctb"),
7 
+            person("Vincent", "Carey", role="ctb"),
8 
+            person("Robert", "Gentleman", role="ctb"),
9 
+            person("Wolfgang", "Huber", role="ctb"),
10 
+            person("Jim", "MacDonald", role="ctb"),
11 
+            person("Harris", "Jaffee", role="ctb"))
12 
+Depends: R (>= 2.14.0),
8 13 
          oligoClasses (>= 1.13.9),
9 14 
          foreach
10 15 
 Imports: affyio (>= 1.19.4),
11 16 
          affxparser (>= 1.23.1),
12 17 
          Biobase (>= 2.11.8),
13 18 
          Biostrings,
19 
+         BiocGenerics,
14 20 
          DBI (>= 0.2-5),
15 21 
          ff,
16 22 
          graphics,
... ... 
@@ -18,6 +24,7 @@ Imports: affyio (>= 1.19.4),
18 24 
          preprocessCore (>= 1.13.5),
19 25 
          splines,
20 26 
          stats,
27 
+         stats4,
21 28 
          utils,
22 29 
          zlibbioc
23 30 
 Enhances: ff,
Browse code

Import boxplot, image, and residuals generics from BiocGenerics.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63484 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/03/2012 19:35:24
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History View file @ 9e19681
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@@ -1,9 +1,10 @@
1 1 
 Package: oligo
2 
-Version: 1.19.13
2 
+Version: 1.19.14
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
7 
+         BiocGenerics (>= 0.1.11),
7 8 
          oligoClasses (>= 1.13.9),
8 9 
          foreach
9 10 
 Imports: affyio (>= 1.19.4),
Browse code

accid. committed wrong branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63025 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2012 17:59:03
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History View file @ 20917b7
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.12-0
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+Version: 1.19.13
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

rewriting fitPLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63018 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2012 17:52:18
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DESCRIPTION
History View file @ 338b0fd
... ... 
@@ -4,7 +4,8 @@ Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
7 
-         oligoClasses (>= 1.13.9)
7 
+         oligoClasses (>= 1.13.9),
8 
+         foreach
8 9 
 Imports: affyio (>= 1.19.4),
9 10 
          affxparser (>= 1.23.1),
10 11 
          Biobase (>= 2.11.8),
Browse code

removing more affyPLM stuff

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63016 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2012 17:52:01
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DESCRIPTION
History View file @ 4f0b360
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@@ -58,7 +58,6 @@ Collate: AllGenerics.R
58 58 
          justCRLMM.R
59 59 
          methods-snp6.R
60 60 
          methods-genotype.R
61 
-         PLM_internal.R
62 61 
          methods-PLMset.R
63 62 
          zzz.R
64 63 
 LazyLoad: Yes
Browse code

Removed C code fom affyPLM / removed fitPLM / doing PLM through preprocessCore soon

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63015 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2012 17:51:52
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DESCRIPTION
History View file @ 8b981d1
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@@ -59,7 +59,6 @@ Collate: AllGenerics.R
59 59 
          methods-snp6.R
60 60 
          methods-genotype.R
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          PLM_internal.R
62 
-         fitPLM.R
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          methods-PLMset.R
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          zzz.R
65 64 
 LazyLoad: Yes
Browse code

tracking: removal of affyPLM C-code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@63014 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2012 17:51:32
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DESCRIPTION
History View file @ 0f2c57d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.19.11
2 
+Version: 1.19.12-0
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

fix whitespace formatting problem

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62605 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 07/02/2012 17:09:07
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 Package: oligo
2 
-Version: 1.19.10
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+Version: 1.19.11
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Merging GitHub and BioC

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62518 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/02/2012 17:17:33
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 Package: oligo
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-Version: 1.19.9
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+Version: 1.19.10
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Now built with Makevars(.win) and make sure that it is not deleted by cleanup(.win). Makevars points to proper libraries, including zlibbioc's version of libz on windows.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62494 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/02/2012 02:19:01
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 Package: oligo
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-Version: 1.19.8
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+Version: 1.19.9
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Adding 1st unit test

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62460 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/02/2012 23:35:31
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 Package: oligo
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-Version: 1.19.7
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+Version: 1.19.8
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -29,7 +29,8 @@ Suggests: hapmap100kxba,
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           genefilter,
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           limma,
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           RColorBrewer,
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-          oligoData
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+          oligoData,
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+          RUnit
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 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
34 35 
 License: LGPL (>= 2)
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 Collate: AllGenerics.R
Browse code

Merge branch 'probeSelectors'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62380 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/01/2012 17:36:19
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 Package: oligo
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-Version: 1.19.6
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+Version: 1.19.7
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Merged cleanup

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62336 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2012 18:11:31
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 Package: oligo
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-Version: 1.19.5-1
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+Version: 1.19.6
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 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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+Author: Benilton Carvalho, Rafael Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber, Harris Jaffee, Jim MacDonald
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
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          oligoClasses (>= 1.13.9)
Browse code

Removed configure* src/Makecars*

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62335 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2012 18:11:23
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 Package: oligo
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-Version: 1.19.5
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+Version: 1.19.5-1
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Improved selector / added file to Collate

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62332 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2012 18:10:58
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 Package: oligo
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-Version: 1.19.4
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -49,6 +49,7 @@ Collate: AllGenerics.R
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          read.celfiles.R
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          read.xysfiles.R
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          utils-general.R
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+         utils-selectors.R
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          todo-snp.R
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          functions-crlmm.R
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          functions-snprma.R
Browse code

Improving implementation of selectors.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62330 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2012 18:10:42
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 Package: oligo
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-Version: 1.19.3
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+Version: 1.19.4
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 Title: Preprocessing tools for oligonucleotide arrays.
4 
-Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
4 
+Author: Benilton Carvalho, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
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          oligoClasses (>= 1.13.9)
Browse code

Allowing for summarization at different levels with fitPLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62217 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/01/2012 13:28:48
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 Package: oligo
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-Version: 1.19.2
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+Version: 1.19.3
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Added pmStrand for Affy-Tiling - by Kristof De Beuf

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@62020 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/01/2012 19:02:48
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

fixed txtMessage error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@61986 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/01/2012 12:53:56
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

version bump for start of 2.10 development cycle

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@59924 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 31/10/2011 23:12:28
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

bumped package version numbers prior to creating 2.9 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@59920 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 31/10/2011 22:59:03
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 Package: oligo
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-Version: 1.17.3
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+Version: 1.18.0
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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fixes to accomodate changes in pdInfoBuilder

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@59591 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/10/2011 00:41:20
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@@ -4,8 +4,7 @@ Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.13.0),
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-         oligoClasses (>= 1.13.9),
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-         preprocessCore (>= 1.13.5)
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+         oligoClasses (>= 1.13.9)
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 Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          ff,
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          graphics,
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          methods,
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          splines,
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@@ -61,4 +61,4 @@ Collate: AllGenerics.R
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          methods-PLMset.R
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          zzz.R
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 LazyLoad: Yes
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-biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
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+biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, ExonArray, GeneExpression, Bioinformatics, DataImport
Browse code

Small bugfix to MAplot(). The plot title was getting concatenated in a loop, and extended to include all chips by the last one.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@57635 bc3139a8-67e5-0310-9ffc-ced21a209358

James MacDonald authored on 24/08/2011 13:35:12
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 Package: oligo
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-Version: 1.17.2
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+Version: 1.17.3
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

use zlibbioc for zlib

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@56179 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 14/06/2011 21:36:25
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -16,7 +16,8 @@ Imports: affyio (>= 1.19.4),
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          methods,
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          splines,
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 Enhances: ff,
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 LinkingTo: preprocessCore
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use $(ZLIB_LIBS) rather than -Rlibz in Makevars.win

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@55189 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 30/04/2011 23:17:17
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54802 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/04/2011 22:36:43
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 Package: oligo
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-Version: 1.16.0
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Bumped version numbers for BioC 2.8 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54800 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/04/2011 22:27:35
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54723 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/04/2011 14:38:09
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 Package: oligo
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-Version: 1.15.14
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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          oligoClasses (>= 1.13.9),
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-         preprocessCore (>= 1.13.5), ff
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+         preprocessCore (>= 1.13.5)
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 Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
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          DBI (>= 0.2-5),
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          methods,
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Fixes on CRLMM and example that BioC Win machine cant run

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54721 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/04/2011 14:05:51
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 Package: oligo
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-Version: 1.15.13
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+Version: 1.15.14
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.13.0),
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          oligoClasses (>= 1.13.9),
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-         preprocessCore (>= 1.13.5)
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+         preprocessCore (>= 1.13.5), ff
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 Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          Biostrings,
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          DBI (>= 0.2-5),
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+         ff (>= 2.2-1),
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          graphics,
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          methods,
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          splines,
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fixing docs and problems with C-code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54653 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/04/2011 01:27:07
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fixing MAplot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54506 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/04/2011 18:56:45
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Fix PLM - summarize

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54337 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/03/2011 20:04:44
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 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Initial implementation of DABG

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54182 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/03/2011 15:46:21
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DESCRIPTION
History View file @ 967fe84
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.15.9
2 
+Version: 1.15.10
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -9,6 +9,7 @@ Depends: R (>= 2.13.0),
9 9 
 Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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+         Biostrings,
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          DBI (>= 0.2-5),
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          graphics,
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          methods,
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@@ -20,6 +21,7 @@ Enhances: ff,
20 21 
 LinkingTo: preprocessCore
21 22 
 Suggests: hapmap100kxba,
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           pd.mapping50k.xba240,
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+          pd.huex.1.0.st.v2,
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           pd.hg18.60mer.expr,
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           maqcExpression4plex,
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           genefilter,
Browse code

fitPLM getting more stable

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54112 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/03/2011 20:07:15
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DESCRIPTION
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1 1 
 Package: oligo
2 
-Version: 1.15.8
2 
+Version: 1.15.9
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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@@ -39,6 +39,9 @@ Collate: AllGenerics.R
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          methods-SnpCnvFeatureSet.R
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          methods-TilingFeatureSet.R
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          methods-DBPDInfo.R
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+         methods-background.R
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+         methods-normalization.R
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+         methods-summarization.R
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          read.celfiles.R
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          read.xysfiles.R
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          utils-general.R
Browse code

adding forgoten files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54075 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/03/2011 08:19:18
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 Package: oligo
2 
-Version: 1.15.7
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+Version: 1.15.8
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Getting ready for QC with PLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@54044 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/03/2011 15:07:50
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DESCRIPTION
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1 1 
 Package: oligo
2 
-Version: 1.15.5
2 
+Version: 1.15.7
3 3 
 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
6 6 
 Depends: R (>= 2.13.0),
7 
-         oligoClasses (>= 1.13.9)
7 
+         oligoClasses (>= 1.13.9),
8 
+         preprocessCore (>= 1.13.5)
8 9 
 Imports: affyio (>= 1.19.4),
9 10 
          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          DBI (>= 0.2-5),
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          graphics,
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          methods,
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-         preprocessCore (>= 1.13.5),
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          splines,
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          stats,
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          utils
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@@ -24,13 +24,15 @@ Suggests: hapmap100kxba,
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           maqcExpression4plex,
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           genefilter,
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           limma,
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-          RColorBrewer
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+          RColorBrewer,
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+          oligoData
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 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
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 License: LGPL (>= 2)
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 Collate: AllGenerics.R
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          methods-GeneFeatureSet.R
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          methods-ExonFeatureSet.R
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          methods-ExpressionFeatureSet.R
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+         methods-ExpressionSet.R
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          methods-LDS.R
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          methods-FeatureSet.R
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          methods-SnpFeatureSet.R
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@@ -47,6 +49,9 @@ Collate: AllGenerics.R
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          justCRLMM.R
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          methods-snp6.R
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          methods-genotype.R
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+         PLM_internal.R
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+         fitPLM.R
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+         methods-PLMset.R
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          zzz.R
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 LazyLoad: Yes
52 57 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
Browse code

details for PLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@53991 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2011 15:17:00
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 Package: oligo
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-Version: 1.15.4
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+Version: 1.15.5
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

updating TODO in org-mode

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@53105 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/02/2011 16:07:55
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DESCRIPTION
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 Package: oligo
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-Version: 1.15.3
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+Version: 1.15.4
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
Browse code

Adding PLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@53053 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/02/2011 15:12:16
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DESCRIPTION
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 Package: oligo
2 
-Version: 1.15.2
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+Version: 1.15.3
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.13.0),
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          oligoClasses (>= 1.13.9)
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-Imports: affyio (>= 1.19.2),
8 
+Imports: affyio (>= 1.19.4),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
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          DBI (>= 0.2-5),
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          graphics,
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          methods,
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-         preprocessCore (>= 1.13.4),
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+         preprocessCore (>= 1.13.5),
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          splines,
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          stats,
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          utils
Browse code

Updating dependencies on oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@51849 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/01/2011 18:18:40
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DESCRIPTION
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@@ -4,7 +4,7 @@ Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.13.0),
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-         oligoClasses (>= 1.13.8)
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+         oligoClasses (>= 1.13.9)
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 Imports: affyio (>= 1.19.2),
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          affxparser (>= 1.23.1),
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          Biobase (>= 2.11.8),
Browse code

Fixing NEWS.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@51844 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/01/2011 12:01:03
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DESCRIPTION
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@@ -1,17 +1,17 @@
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 Package: oligo
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-Version: 1.15.1
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+Version: 1.15.2
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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-Depends: R (>= 2.11.0),
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-Imports: affyio (>= 1.19.1),
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-         affxparser (>= 1.17.3),
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-         Biobase (>= 2.7.3),
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-         DBI (>= 0.2-4),
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+Depends: R (>= 2.13.0),
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+         oligoClasses (>= 1.13.8)
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+Imports: affyio (>= 1.19.2),
9 
+         affxparser (>= 1.23.1),
10 
+         Biobase (>= 2.11.8),
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+         DBI (>= 0.2-5),
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          graphics,
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          methods,
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-         preprocessCore (>= 1.9.0),
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+         preprocessCore (>= 1.13.4),
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          splines,
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          stats,
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          utils
Browse code

Prep-ing new code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@50817 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/11/2010 12:19:10
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DESCRIPTION
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@@ -5,7 +5,7 @@ Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry
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 Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.11.0),
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          oligoClasses (>= 1.9.41)
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-Imports: affyio (>= 1.15.2),
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+Imports: affyio (>= 1.19.1),
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          affxparser (>= 1.17.3),
10 10 
          Biobase (>= 2.7.3),
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          DBI (>= 0.2-4),
Browse code

Preping for new stuff

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@50555 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/10/2010 14:59:20
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@@ -1,8 +1,8 @@
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 Package: oligo
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-Version: 1.15.0
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+Version: 1.15.1
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 Title: Preprocessing tools for oligonucleotide arrays.
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-Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 
-Maintainer: Benilton Carvalho <carvalho@bclab.org>
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+Author: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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+Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 Depends: R (>= 2.11.0),
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          oligoClasses (>= 1.9.41)
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 Imports: affyio (>= 1.15.2),
Browse code

Bumped version numbers again for new BioC 2.8 devel cycle. ERRATA: Previous bump was for BioC 2.7 release (of course), not 2.6!

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@50295 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/10/2010 05:57:44
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 Package: oligo
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-Version: 1.14.0
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bumped version numbers for BioC 2.6 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@50293 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/10/2010 05:34:23
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

added getNetAffx and fixed bugs with basicFeatureData/basicPh1/basicPh2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@50150 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/10/2010 11:11:28
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Added citation information

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@48853 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/08/2010 10:05:31
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 Package: oligo
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-Version: 1.13.6
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Added date/time to protocolData

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@48708 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/08/2010 17:16:58
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bug fixes in boxplot for ExpressionSets

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@47355 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/06/2010 11:00:38
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bug fixes in configure

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@47088 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/05/2010 14:33:58
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-Version: 1.13.3
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

bugs with subsetting

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@47085 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/05/2010 10:04:07
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 Package: oligo
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-Version: 1.13.2
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@47046 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/05/2010 11:49:01
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@@ -16,8 +16,7 @@ Imports: affyio (>= 1.15.2),
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 Enhances: ff,
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba,
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           pd.mapping50k.xba240,
Browse code

Bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@47045 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/05/2010 10:48:14
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 Package: oligo
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-Version: 1.13.1
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+Version: 1.13.2
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 Title: Preprocessing tools for oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba,
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           pd.mapping50k.xba240,
Browse code

Bug fixes due to changes in annotation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46718 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/05/2010 00:15:41
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bumped version numbers for BioC 2.7 trunk

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46405 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 22/04/2010 18:45:15
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Bumped version numbers for BioC 2.6 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46401 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 22/04/2010 18:21:23
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

fixed docs/vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46348 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/04/2010 01:51:27
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Extended hist/boxplot/image for FeatureSet's to properly plot N-color data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46308 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/04/2010 16:00:50
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

revised man page for rma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46206 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/04/2010 16:10:41
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 Package: oligo
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Modified CONTAINER location (now in (pm/bg)feature table)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46093 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/04/2010 13:32:53
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Update for transfer

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@46090 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/04/2010 11:10:37
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 Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

NEWS @ inst/

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45815 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/04/2010 11:01:11
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Fixed warning for getM/getA on TilingFeatureSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45759 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/04/2010 15:29:35
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

pass check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45593 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/03/2010 15:53:52
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 Package: oligo
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-Version: 1.11.32
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-Title: Oligonucleotide arrays tools.
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+Title: Preprocessing tools for oligonucleotide arrays.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 6 
 Depends: R (>= 2.11.0),
Browse code

Fixed ordering for probeNames - gene/exon arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45392 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/03/2010 11:27:04
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Cleaning up code after moving stuff to oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45170 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/03/2010 15:03:54
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 Package: oligo
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-Version: 1.11.30
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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          read.celfiles.R
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          read.xysfiles.R
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          utils-general.R
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          todo-snp.R
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          functions-crlmm.R
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Browse code

Replaced oLapply by ocLapply

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45167 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/03/2010 11:37:00
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-Version: 1.11.29
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Moved docs (cluster) to oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45162 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/03/2010 00:19:57
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Moving cluster tools from oligo to oligoClasses, so crlmm can also benefit from them

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45148 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2010 21:43:52
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 Package: oligo
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-Version: 1.11.27
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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 Depends: R (>= 2.11.0),
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 Imports: affyio (>= 1.15.2),
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          affxparser (>= 1.17.3),
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Browse code

Started moving tools for ff and snow from oligo to oligoClasses so they can be used also in crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45135 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2010 17:42:52
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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Adding ff/parallel support to snprma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45053 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/03/2010 15:51:35
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1 1 
 Package: oligo
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-Version: 1.11.26
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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 Imports: affyio (>= 1.15.2),
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          affxparser (>= 1.17.3),
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          Biobase (>= 2.7.3),
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          DBI (>= 0.2-4),
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          graphics,
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          methods,
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          functions-crlmm.R
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          functions-snprma.R
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          justSNPRMA.R
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45033 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/03/2010 15:20:56
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45032 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/03/2010 15:19:02
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

several changes in oligo/oligoClasses/pdInfoBuilder

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@45031 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/03/2010 14:49:27
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1 1 
 Package: oligo
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-Version: 1.11.22
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+Version: 1.11.24
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 Title: Oligonucleotide arrays tools.
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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-         oligoClasses (>= 1.9.25),
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 Imports: affyio (>= 1.15.2),
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          affxparser (>= 1.17.3),
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          Biobase (>= 2.7.3),
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          DBI (>= 0.2-4),
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          graphics,
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          methods,
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+         oligoClasses (>= 1.9.25),
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          splines,
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          stats,
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          utils
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Fixed vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44947 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/03/2010 17:10:26
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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Fixing vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44946 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/03/2010 17:03:44
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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Fixed getFid* to accomodate changes in the annotation pkg / added probeNames for Exon/Gene arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44945 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/03/2010 16:12:46
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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Fixed Makefile

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44928 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/02/2010 17:07:39
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5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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Added functions used in paper / Added hands-on vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44912 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/02/2010 23:31:03
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1 1 
 Package: oligo
2 
-Version: 1.11.17
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-Title: Tools for low-level analysis of oligonucleotide arrays.
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+Version: 1.11.18
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+Title: Oligonucleotide arrays tools.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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          splines,
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 Enhances: ff,
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           snow
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 LinkingTo: preprocessCore
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           genefilter,
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           limma,
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           RColorBrewer
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-Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
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+Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
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 Collate: AllGenerics.R
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          methods-GeneFeatureSet.R
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          read.xysfiles.R
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          utils-cluster.R
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          justSNPRMA.R
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          justCRLMM.R
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          methods-snp6.R
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Fixed NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44767 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/02/2010 13:40:29
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 Package: oligo
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-Version: 1.11.16
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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-Depends: R (>= 2.11.0), oligoClasses (>= 1.9.25), preprocessCore (>= 1.9.0)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.2)
8 
-Enhances: ff, snow
6 
+Depends: R (>= 2.11.0),
7 
+         oligoClasses (>= 1.9.25),
8 
+         preprocessCore (>= 1.9.0)
9 
+Imports: affyio (>= 1.15.2),
10 
+         affxparser (>= 1.17.3),
11 
+         Biobase (>= 2.7.3),
12 
+         DBI (>= 0.2-4),
13 
+         graphics,
14 
+         methods,
15 
+         splines,
16 
+         stats,
17 
+         utils,
18 
+Enhances: ff,
19 
+          snow
9 20 
 LinkingTo: preprocessCore
10 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
21 
+Suggests: hapmap100kxba,
22 
+          pd.mapping50k.xba240,
23 
+          pd.hg18.60mer.expr,
24 
+          maqcExpression4plex,
25 
+          genefilter,
26 
+          limma,
27 
+          RColorBrewer
11 28 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 29 
 License: LGPL (>= 2)
13 30 
 Collate: AllGenerics.R
Browse code

Fixed Collate and filenames

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44755 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/02/2010 00:03:42
Showing 1 changed files
DESCRIPTION
History View file @ 09c46f8
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.15
2 
+Version: 1.11.16
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
... ... 
@@ -11,11 +11,10 @@ Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpressio
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL (>= 2)
13 13 
 Collate: AllGenerics.R
14 
-         methods-bigmemory.R
15 14 
          methods-GeneFeatureSet.R
16 15 
          methods-ExonFeatureSet.R
17 16 
          methods-ExpressionFeatureSet.R
18 
-         methods-large.R
17 
+         methods-LDS.R
19 18 
          methods-FeatureSet.R
20 19 
          methods-SnpFeatureSet.R
21 20 
          methods-SnpCnvFeatureSet.R
... ... 
@@ -23,7 +22,6 @@ Collate: AllGenerics.R
23 22 
          methods-DBPDInfo.R
24 23 
          read.celfiles.R
25 24 
          read.xysfiles.R
26 
-         zzz.R
27 25 
          utils-general.R
28 26 
          utils-cluster.R
29 27 
          crlmm.R
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@@ -32,5 +30,6 @@ Collate: AllGenerics.R
32 30 
          justCRLMM.R
33 31 
          methods-snp6.R
34 32 
          methods-genotype.R
33 
+         zzz.R
35 34 
 LazyLoad: Yes
36 35 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
Browse code

Replaced bigmemory by ff

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44754 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/02/2010 23:59:47
Showing 1 changed files
DESCRIPTION
History View file @ 065954a
... ... 
@@ -1,11 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 1.11.14
2 
+Version: 1.11.15
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 6 
 Depends: R (>= 2.11.0), oligoClasses (>= 1.9.25), preprocessCore (>= 1.9.0)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.2), digest
8 
-Enhances: bigmemory (>= 4.0.0), snow
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.2)
8 
+Enhances: ff, snow
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
... ... 
@@ -15,6 +15,7 @@ Collate: AllGenerics.R
15 15 
          methods-GeneFeatureSet.R
16 16 
          methods-ExonFeatureSet.R
17 17 
          methods-ExpressionFeatureSet.R
18 
+         methods-large.R
18 19 
          methods-FeatureSet.R
19 20 
          methods-SnpFeatureSet.R
20 21 
          methods-SnpCnvFeatureSet.R
Browse code

Exported pmChr / fixed .onAttach

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44647 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/02/2010 11:08:56
Showing 1 changed files
DESCRIPTION
History View file @ 68f5908
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@@ -1,10 +1,10 @@
1 1 
 Package: oligo
2 
-Version: 1.11.12
2 
+Version: 1.11.14
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 6 
 Depends: R (>= 2.11.0), oligoClasses (>= 1.9.25), preprocessCore (>= 1.9.0)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.1), digest
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.2), digest
8 8 
 Enhances: bigmemory (>= 4.0.0), snow
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
Browse code

Fixed selection of bg probes on Exon/Gene chips so it obeys the MPS files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44435 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/02/2010 15:55:11
Showing 1 changed files
DESCRIPTION
History View file @ 976226e
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.11
2 
+Version: 1.11.12
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

major changes to oligo: large dataset support with bigmemory + some parallel code through snow

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@44375 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/01/2010 20:38:58
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DESCRIPTION
History View file @ 92e3ddf
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@@ -1,15 +1,17 @@
1 1 
 Package: oligo
2 
-Version: 1.11.9
2 
+Version: 1.11.11
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 
-Depends: R (>= 2.10.0), oligoClasses (>= 1.9.14), preprocessCore (>= 1.7.4)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
6 
+Depends: R (>= 2.11.0), oligoClasses (>= 1.9.25), preprocessCore (>= 1.9.0)
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.1), digest
8 
+Enhances: bigmemory (>= 4.0.0), snow
8 9 
 LinkingTo: preprocessCore
9 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 12 
 License: LGPL (>= 2)
12 13 
 Collate: AllGenerics.R
14 
+         methods-bigmemory.R
13 15 
          methods-GeneFeatureSet.R
14 16 
          methods-ExonFeatureSet.R
15 17 
          methods-ExpressionFeatureSet.R
... ... 
@@ -19,9 +21,10 @@ Collate: AllGenerics.R
19 21 
          methods-TilingFeatureSet.R
20 22 
          methods-DBPDInfo.R
21 23 
          read.celfiles.R
24 
+         read.xysfiles.R
22 25 
          zzz.R
23 
-         readxys.R
24 
-         utils.R
26 
+         utils-general.R
27 
+         utils-cluster.R
25 28 
          crlmm.R
26 29 
          snprma.R
27 30 
          justSNPRMA.R
Browse code

undoing changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43856 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/01/2010 10:13:25
Showing 1 changed files
DESCRIPTION
History View file @ ca3cbf8
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@@ -1,11 +1,10 @@
1 1 
 Package: oligo
2 
-Version: 1.11.10
2 
+Version: 1.11.9
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 
-Depends: R (>= 2.11.0), oligoClasses (>= 1.9.24), preprocessCore (>= 1.9.0)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.1)
8 
-Enhances: bigmemory
6 
+Depends: R (>= 2.10.0), oligoClasses (>= 1.9.14), preprocessCore (>= 1.7.4)
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
9 8 
 LinkingTo: preprocessCore
10 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
11 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

ensuring specific pkg versions are used

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43855 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/01/2010 09:52:49
Showing 1 changed files
DESCRIPTION
History View file @ 897b251
... ... 
@@ -1,10 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 1.11.9
2 
+Version: 1.11.10
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 
-Depends: R (>= 2.10.0), oligoClasses (>= 1.9.14), preprocessCore (>= 1.7.4)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
6 
+Depends: R (>= 2.11.0), oligoClasses (>= 1.9.24), preprocessCore (>= 1.9.0)
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.7.3), methods, affyio (>= 1.15.1)
8 
+Enhances: bigmemory
8 9 
 LinkingTo: preprocessCore
9 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Updating requirements

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43391 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/12/2009 16:39:35
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DESCRIPTION
History View file @ 4cf3c25
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@@ -1,9 +1,9 @@
1 1 
 Package: oligo
2 
-Version: 1.11.8
2 
+Version: 1.11.9
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 
-Depends: R (>= 2.10.0), oligoClasses (>= 1.7.12), preprocessCore (>= 1.7.4)
6 
+Depends: R (>= 2.10.0), oligoClasses (>= 1.9.14), preprocessCore (>= 1.7.4)
7 7 
 Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
8 8 
 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
Browse code

Updating notes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43382 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/12/2009 04:23:54
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DESCRIPTION
History View file @ 8b7f5f8
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.7
2 
+Version: 1.11.8
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

syncing documentation from oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43381 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/12/2009 04:17:22
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.6
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+Version: 1.11.7
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Moved some methods from oligoClasses->oligo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43344 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/12/2009 14:33:00
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DESCRIPTION
History View file @ 7c04fbf
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.5
2 
+Version: 1.11.6
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Reorganizing package methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43310 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/12/2009 02:48:08
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.4
2 
+Version: 1.11.5
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
... ... 
@@ -14,6 +14,7 @@ Collate: AllGenerics.R
14 14 
          methods-ExonFeatureSet.R
15 15 
          methods-ExpressionFeatureSet.R
16 16 
          methods-FeatureSet.R
17 
+         methods-SnpFeatureSet.R
17 18 
          methods-SnpCnvFeatureSet.R
18 19 
          methods-TilingFeatureSet.R
19 20 
          methods-DBPDInfo.R
Browse code

reorganization of classes used by oligoClasses and oligo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@43304 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/11/2009 21:24:40
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History View file @ 060efcb
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.11.3
2 
+Version: 1.11.4
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

added rma() for quick and informal inspection of CNPs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42936 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/11/2009 20:14:02
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1 1 
 Package: oligo
2 
-Version: 1.11.2
2 
+Version: 1.11.3
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
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@@ -14,6 +14,7 @@ Collate: AllGenerics.R
14 14 
          methods-ExonFeatureSet.R
15 15 
          methods-ExpressionFeatureSet.R
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          methods-FeatureSet.R
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+         methods-SnpCnvFeatureSet.R
17 18 
          methods-TilingFeatureSet.R
18 19 
          methods-DBPDInfo.R
19 20 
          read.celfiles.R
Browse code

Cleaning up the package to use preprocessCore functions more effectively

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42864 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/11/2009 02:04:31
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History View file @ 630aa6a
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1 1 
 Package: oligo
2 
-Version: 1.11.0
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+Version: 1.11.2
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Package version bump for BioC 2.6 devel.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42686 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 27/10/2009 23:45:24
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 Package: oligo
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-Version: 1.10.0
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+Version: 1.11.0
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Package version bump for BioC 2.5 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42684 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 27/10/2009 23:33:29
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 Package: oligo
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-Version: 1.9.26
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+Version: 1.10.0
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Internal updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42673 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/10/2009 14:13:56
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-Version: 1.9.25
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+Version: 1.9.26
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Minor internal updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42632 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/10/2009 23:45:38
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 Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <carvalho@bclab.org>
Browse code

Fixed vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@42528 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/10/2009 06:02:51
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 Package: oligo
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 
-Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 
-Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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+Author: Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
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+Maintainer: Benilton Carvalho <carvalho@bclab.org>
6 6 
 Depends: R (>= 2.10.0), oligoClasses (>= 1.7.12), preprocessCore (>= 1.7.4)
7 7 
 Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
8 8 
 LinkingTo: preprocessCore
Browse code

Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41539 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 06/09/2009 03:06:55
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 Package: oligo
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 
-License: LGPL version 2 or newer
11 
+License: LGPL (>= 2)
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 Collate: AllGenerics.R
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          methods-GeneFeatureSet.R
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          methods-ExonFeatureSet.R
Browse code

Added more details to docs of list.xysfiles and list.celfiles

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41259 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/08/2009 02:31:58
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 Title: Tools for low-level analysis of oligonucleotide arrays.
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed boxplot for ExpressionSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41240 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/08/2009 02:21:50
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed image() for Affymetrix arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41181 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/08/2009 04:20:33
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Exposing requireAnnotation and pkg downloader

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41083 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/08/2009 17:23:58
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-Depends: R (>= 2.10.0), oligoClasses (>= 1.7.10), preprocessCore (>= 1.7.4)
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+Depends: R (>= 2.10.0), oligoClasses (>= 1.7.12), preprocessCore (>= 1.7.4)
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 Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
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 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
Browse code

Improving support to Gene/Exon Arrays - gene level summaries

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41065 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/08/2009 22:23:36
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added automatic installer/downloader

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@41034 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/08/2009 05:19:16
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: R (>= 2.10.0), oligoClasses (>= 1.7.9), preprocessCore (>= 1.7.4)
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+Depends: R (>= 2.10.0), oligoClasses (>= 1.7.10), preprocessCore (>= 1.7.4)
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 Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
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 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
Browse code

Forgot to update pkg version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@40953 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/08/2009 05:06:33
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 Title: Tools for low-level analysis of oligonucleotide arrays.
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed version for affyio

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@40936 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/07/2009 13:06:12
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.10.0), oligoClasses (>= 1.7.9), preprocessCore (>= 1.7.4)
7 
-Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.17.3)
7 
+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.13.3)
8 8 
 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Removed warnings at the C-level and added more strict structure of versions of dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@40931 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/07/2009 04:58:43
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Imports: splines, affxparser (>= 1.17.2), graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
6 
+Depends: R (>= 2.10.0), oligoClasses (>= 1.7.9), preprocessCore (>= 1.7.4)
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+Imports: splines, affxparser (>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase (>= 2.5.5), methods, affyio (>= 1.17.3)
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

typo function name

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39881 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/06/2009 16:54:20
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed problem with basicRMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39827 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/06/2009 02:59:51
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed bug in getMetadata2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39418 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/05/2009 14:49:28
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

date/time added to FeatureSet objects

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39401 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/05/2009 19:26:13
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 Title: Tools for low-level analysis of oligonucleotide arrays.
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.8.0), oligoClasses (>= 1.7.2), preprocessCore
7 
-Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
7 
+Imports: splines, affxparser (>= 1.17.2), graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Fixed problems with sampleNames, which caused rma() to fail

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39382 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/05/2009 03:46:16
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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+Depends: R (>= 2.8.0), oligoClasses (>= 1.7.2), preprocessCore
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 Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
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 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
Browse code

Removed extra ordering in XYS parser

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39372 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/05/2009 16:25:03
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

XYS parser at C-level / fixed bug with sampleNames being ignored

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39370 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/05/2009 15:57:48
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Changed error message (when annotation cannot be loaded)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39337 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/05/2009 19:24:29
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39207 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/04/2009 05:46:32
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added getContainer help page

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39116 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/04/2009 17:27:15
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added extractor for relevant field for NGS arrays: getContainer

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39107 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/04/2009 18:55:08
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing version...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39082 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/04/2009 21:41:21
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          utils.R
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          crlmm.R
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-	     justSNPRMA.R
26 
-	     justCRLMM.R
25 
+         justSNPRMA.R
26 
+         justCRLMM.R
27 27 
          methods-snp6.R
28 28 
          methods-genotype.R
29 29 
 LazyLoad: Yes
Browse code

Bumped pkg versions for BioC 2.5 devel line.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39015 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 20/04/2009 23:44:07
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.8.0
2 
+Version: 1.9.0
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Bumped pkg versions for BioC 2.4 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@39013 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 20/04/2009 23:24:12
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1 1 
 Package: oligo
2 
-Version: 1.7.43
2 
+Version: 1.8.0
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Reverted back last checkin.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38902 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 16/04/2009 19:13:53
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@@ -1,12 +1,12 @@
1 1 
 Package: oligo
2 
-Version: 1.7.44
2 
+Version: 1.7.43
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.8.0), oligoClasses (>= 1.5.22), preprocessCore
7 7 
 Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
9 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 11 
 License: LGPL version 2 or newer
12 12 
 Collate: AllGenerics.R
... ... 
@@ -22,8 +22,8 @@ Collate: AllGenerics.R
22 22 
          utils.R
23 23 
          crlmm.R
24 24 
          snprma.R
25 
-	 justSNPRMA.R
26 
-	 justCRLMM.R
25 
+	     justSNPRMA.R
26 
+	     justCRLMM.R
27 27 
          methods-snp6.R
28 28 
          methods-genotype.R
29 29 
 LazyLoad: Yes
Browse code

geneplotter is needed for vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38897 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/04/2009 17:55:10
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1 1 
 Package: oligo
2 
-Version: 1.7.43
2 
+Version: 1.7.44
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.8.0), oligoClasses (>= 1.5.22), preprocessCore
7 7 
 Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
9 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 11 
 License: LGPL version 2 or newer
12 12 
 Collate: AllGenerics.R
Browse code

Removed unneeded geneplotter dependency.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38871 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 16/04/2009 04:47:52
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@@ -6,7 +6,7 @@ Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.8.0), oligoClasses (>= 1.5.22), preprocessCore
7 7 
 Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
9 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 11 
 License: LGPL version 2 or newer
12 12 
 Collate: AllGenerics.R
Browse code

Cleaning up code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38866 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/04/2009 04:10:51
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History View file @ e1bd582
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@@ -1,9 +1,9 @@
1 1 
 Package: oligo
2 
-Version: 1.7.42
2 
+Version: 1.7.43
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.5.0), oligoClasses (>= 1.5.9), preprocessCore
6 
+Depends: R (>= 2.8.0), oligoClasses (>= 1.5.22), preprocessCore
7 7 
 Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
... ... 
@@ -28,4 +28,3 @@ Collate: AllGenerics.R
28 28 
          methods-genotype.R
29 29 
 LazyLoad: Yes
30 30 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
31 
-
Browse code

Fixed warning: documentation for getX/getY

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38829 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/04/2009 18:31:47
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1 1 
 Package: oligo
2 
-Version: 1.7.41
2 
+Version: 1.7.42
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing problem when writing analysis.txt

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38804 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/04/2009 23:06:38
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1 1 
 Package: oligo
2 
-Version: 1.7.40
2 
+Version: 1.7.41
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Improved memory usage for 250K arrays - CRLMM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38793 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/04/2009 19:46:07
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1 1 
 Package: oligo
2 
-Version: 1.7.38
2 
+Version: 1.7.40
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing accessors for coordinates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38736 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/04/2009 19:28:18
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1 1 
 Package: oligo
2 
-Version: 1.7.37
2 
+Version: 1.7.38
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
... ... 
@@ -15,6 +15,7 @@ Collate: AllGenerics.R
15 15 
          methods-ExpressionFeatureSet.R
16 16 
          methods-FeatureSet.R
17 17 
          methods-TilingFeatureSet.R
18 
+         methods-DBPDInfo.R
18 19 
          read.celfiles.R
19 20 
          zzz.R
20 21 
          readxys.R
Browse code

Cleaned up code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38587 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/04/2009 03:44:32
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.36
2 
+Version: 1.7.37
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -15,7 +15,6 @@ Collate: AllGenerics.R
15 15 
          methods-ExpressionFeatureSet.R
16 16 
          methods-FeatureSet.R
17 17 
          methods-TilingFeatureSet.R
18 
-         methods-SnpCnvFeatureSet.R
19 18 
          read.celfiles.R
20 19 
          zzz.R
21 20 
          readxys.R
Browse code

list.celfiles also returns compressed cel files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38513 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/04/2009 19:20:02
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1 1 
 Package: oligo
2 
-Version: 1.7.35
2 
+Version: 1.7.36
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added affyio, so the read.celfiles is faster and also reads CEL.gz files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38448 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/04/2009 02:14:27
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1 1 
 Package: oligo
2 
-Version: 1.7.34
2 
+Version: 1.7.35
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.5.0), oligoClasses (>= 1.5.9), preprocessCore
7 
-Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods
7 
+Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio
8 8 
 LinkingTo: preprocessCore
9 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
10 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Improved NAMESPACE / Added basicRMA()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38233 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/03/2009 18:08:23
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1 1 
 Package: oligo
2 
-Version: 1.7.30
2 
+Version: 1.7.34
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 
-         splines, RSQLite, preprocessCore, AnnotationDbi,
8 
-         affxparser, oligoClasses (>= 1.5.9)
6 
+Depends: R (>= 2.5.0), oligoClasses (>= 1.5.9), preprocessCore
7 
+Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods
9 8 
 LinkingTo: preprocessCore
10 9 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
11 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38217 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/03/2009 03:27:20
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1 1 
 Package: oligo
2 
-Version: 1.7.29
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+Version: 1.7.30
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38147 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2009 18:23:05
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 Package: oligo
2 
-Version: 1.7.28
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+Version: 1.7.29
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Updated TODO

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38095 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/03/2009 20:26:39
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1 1 
 Package: oligo
2 
-Version: 1.7.27
2 
+Version: 1.7.28
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
... ... 
@@ -28,4 +28,5 @@ Collate: AllGenerics.R
28 28 
          methods-snp6.R
29 29 
          methods-genotype.R
30 30 
 LazyLoad: Yes
31 
-biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression
31 
+biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
32 
+
Browse code

Removing unneeded code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38077 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/03/2009 03:29:06
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1 1 
 Package: oligo
2 
-Version: 1.7.26
2 
+Version: 1.7.27
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
... ... 
@@ -11,7 +11,6 @@ Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpressio
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
14 
-         methods-platformDesign.R
15 14 
          methods-GeneFeatureSet.R
16 15 
          methods-ExonFeatureSet.R
17 16 
          methods-ExpressionFeatureSet.R
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38065 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/03/2009 18:28:23
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-Version: 1.7.25
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+Version: 1.7.26
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 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added support to HT_HGU_133+ Array

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@38009 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/03/2009 22:58:44
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1 1 
 Package: oligo
2 
-Version: 1.7.24
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+Version: 1.7.25
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 7 
          splines, RSQLite, preprocessCore, AnnotationDbi,
8 
-         affxparser, oligoClasses (>= 1.5.8)
8 
+         affxparser, oligoClasses (>= 1.5.9)
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Improved support for NimbleGen Expression Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37978 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/03/2009 19:02:22
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1 1 
 Package: oligo
2 
-Version: 1.7.23
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+Version: 1.7.24
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 7 
          splines, RSQLite, preprocessCore, AnnotationDbi,
8 
-         affxparser, oligoClasses (>= 1.5.3)
8 
+         affxparser, oligoClasses (>= 1.5.8)
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Much better support to Exon/Gene Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37873 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/03/2009 17:44:36
Showing 1 changed files
DESCRIPTION
History View file @ 34cd2c8
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.21
2 
+Version: 1.7.23
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -12,6 +12,7 @@ Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
14 14 
          methods-platformDesign.R
15 
+         methods-GeneFeatureSet.R
15 16 
          methods-ExonFeatureSet.R
16 17 
          methods-ExpressionFeatureSet.R
17 18 
          methods-FeatureSet.R
Browse code

Cleaning up

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37829 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/03/2009 00:30:13
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DESCRIPTION
History View file @ 70db0c1
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@@ -11,7 +11,6 @@ Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpressio
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
14 
-         basecontent.R
15 14 
          methods-platformDesign.R
16 15 
          methods-ExonFeatureSet.R
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          methods-ExpressionFeatureSet.R
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21 20 
          read.celfiles.R
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          zzz.R
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24 
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          utils.R
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          snprma.R
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 	 justCRLMM.R
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          methods-snp6.R
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          methods-genotype.R
32 
-         m2snp6.R
33 30 
 LazyLoad: Yes
34 31 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression
Browse code

Fixing requirements for RMA on Exon arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37827 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/03/2009 00:11:43
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DESCRIPTION
History View file @ be79e1d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.19
2 
+Version: 1.7.21
3 3 
 Title: Tools for low-level analysis of oligonucleotide arrays.
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -31,4 +31,4 @@ Collate: AllGenerics.R
31 31 
          methods-genotype.R
32 32 
          m2snp6.R
33 33 
 LazyLoad: Yes
34 
-biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
34 
+biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression
Browse code

Improved support for Affy Exon arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37819 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/03/2009 05:53:40
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DESCRIPTION
History View file @ e6596bf
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@@ -1,7 +1,7 @@
1 1 
 Package: oligo
2 
-Version: 1.7.18
3 
-Title: Oligonucleotide Arrays
4 
-Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
2 
+Version: 1.7.19
3 
+Title: Tools for low-level analysis of oligonucleotide arrays.
4 
+Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
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          splines, RSQLite, preprocessCore, AnnotationDbi,
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@@ -13,6 +13,8 @@ License: LGPL version 2 or newer
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 Collate: AllGenerics.R
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          basecontent.R
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          methods-platformDesign.R
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17 
+         methods-ExpressionFeatureSet.R
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          methods-FeatureSet.R
17 19 
          methods-TilingFeatureSet.R
18 20 
          methods-SnpCnvFeatureSet.R
Browse code

Fixing vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37599 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/02/2009 03:26:05
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DESCRIPTION
History View file @ a74462f
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.17
2 
+Version: 1.7.18
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
... ... 
@@ -7,7 +7,7 @@ Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
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          splines, RSQLite, preprocessCore, AnnotationDbi,
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9 9 
 LinkingTo: preprocessCore
10 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex
10 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, geneplotter, limma, RColorBrewer
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
Browse code

Fixing Suggests so expression/ngs vignette workd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37346 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/02/2009 21:23:58
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DESCRIPTION
History View file @ a5719b3
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.16
2 
+Version: 1.7.17
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -7,7 +7,7 @@ Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 7 
          splines, RSQLite, preprocessCore, AnnotationDbi,
8 8 
          affxparser, oligoClasses (>= 1.5.3)
9 9 
 LinkingTo: preprocessCore
10 
-Suggests: hapmap100kxba, pd.mapping50k.xba240
10 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
Browse code

Prep'ing to add 2nd version of db-based annotation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37331 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/02/2009 04:16:10
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DESCRIPTION
History View file @ 1ebc4c7
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.15
2 
+Version: 1.7.16
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fix for RMA on Exon

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37321 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/02/2009 19:33:40
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DESCRIPTION
History View file @ c825485
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1 1 
 Package: oligo
2 
-Version: 1.7.14
2 
+Version: 1.7.15
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added vignette for analysis of NimbleGen Expression data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37160 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/02/2009 02:35:02
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DESCRIPTION
History View file @ 4429ac9
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.13
2 
+Version: 1.7.14
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Bumping versions...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37104 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/02/2009 20:25:40
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DESCRIPTION
History View file @ 775c58b
... ... 
@@ -1,11 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 1.7.12
2 
+Version: 1.7.13
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 7 
          splines, RSQLite, preprocessCore, AnnotationDbi,
8 
-         affxparser, oligoClasses (>= 1.5.1)
8 
+         affxparser, oligoClasses (>= 1.5.3)
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Moving accessors from oligo to oligoClasses - Improving documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37103 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/02/2009 20:24:44
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DESCRIPTION
History View file @ dab355f
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@@ -12,7 +12,6 @@ Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllGenerics.R
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          basecontent.R
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          methods-platformDesign.R
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          methods-FeatureSet.R
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          methods-TilingFeatureSet.R
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          readxys.R
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          sequence.R
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          utils.R
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          crlmm.R
27 
-         show-methods.R
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          snprma.R
29 26 
 	 justSNPRMA.R
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 	 justCRLMM.R
Browse code

Fixed dependency on filenames arg

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37085 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/02/2009 22:06:57
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DESCRIPTION
History View file @ 9a3318b
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.11
2 
+Version: 1.7.12
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixed getPlatformDesign method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37082 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/02/2009 22:04:50
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DESCRIPTION
History View file @ b5eb692
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1 1 
 Package: oligo
2 
-Version: 1.7.10
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+Version: 1.7.11
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Bumping version so some changes are propagated

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@37081 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/02/2009 21:29:32
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DESCRIPTION
History View file @ d0521a3
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.7.9
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+Version: 1.7.10
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Moved many accessors from oligo to oligoClasses. Improving organization, prep'ing to add more meaningful documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@36987 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/01/2009 21:32:25
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DESCRIPTION
History View file @ bdab42f
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@@ -5,13 +5,12 @@ Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
7 7 
          splines, RSQLite, preprocessCore, AnnotationDbi,
8 
-         affxparser, oligoClasses (>= 1.1.18)
8 
+         affxparser, oligoClasses (>= 1.5.1)
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 
-Collate: AllClasses.R
14 
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+Collate: AllGenerics.R
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          basecontent.R
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          readxys.R
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          crlmm.R
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          show-methods.R
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          methods-genotype.R
35 
-         trash.R
36 33 
          m2snp6.R
37 34 
 LazyLoad: Yes
38 35 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Fixing image()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@36960 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/01/2009 16:04:28
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History View file @ 1205ff0
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1 1 
 Package: oligo
2 
-Version: 1.7.8
2 
+Version: 1.7.9
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixed some issues using VECTOR_ELT when STRING_ELT was meant (this is now an error). Docs need help --- someone

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@36914 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Gentleman authored on 22/01/2009 19:52:53
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History View file @ 8f20271
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1 1 
 Package: oligo
2 
-Version: 1.7.7
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+Version: 1.7.8
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fix pmPosition accessor

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35994 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/12/2008 20:05:51
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History View file @ 35e7995
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1 1 
 Package: oligo
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-Version: 1.7.6
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+Version: 1.7.7
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Updated chrom info in featureSet for NGS and fixed pmChr accessor

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35909 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/12/2008 19:53:15
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History View file @ b38d844
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1 1 
 Package: oligo
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-Version: 1.7.5
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+Version: 1.7.6
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Cleaned up read.celfiles, fixed bug with snr and vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35767 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/12/2008 05:58:25
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History View file @ 3801c2c
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1 1 
 Package: oligo
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-Version: 1.7.3
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+Version: 1.7.5
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing probe selection so oligo yelds the same results as affy when running RMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35575 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/12/2008 15:02:45
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History View file @ 3a8d8bd
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1 1 
 Package: oligo
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-Version: 1.7.2
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+Version: 1.7.3
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Added man_fsetid when ordering objects

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35494 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/11/2008 17:32:09
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Browse code

added extra options for readSummaries

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@35481 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/11/2008 01:24:50
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Bumping version numbers for BioC 2.4 devel.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@34814 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 21/10/2008 22:46:31
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Bumping version numbers for BioC 2.3 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@34811 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 21/10/2008 22:32:58
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Browse code

Added missing docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@34306 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/10/2008 09:03:13
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Prep'ing for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@34301 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/10/2008 07:16:32
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reducing memory usage for SNP 6.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@33024 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/08/2008 16:10:46
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Removing an extra object to help reducing RAM usage when processing SNP 6.0 data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@32990 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/08/2008 04:59:04
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Fixed a problem with boxplot on ExpressionSets

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@32390 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/06/2008 06:36:01
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Browse code

Improvements for support of TIling Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@32074 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/06/2008 16:48:55
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5 5 
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Browse code

Adding helper functions for tiling

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31687 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/05/2008 19:16:54
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5 5 
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Browse code

Cleaning up code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31644 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/05/2008 15:47:59
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36 37 
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Browse code

Updating the version number for the trunk post-BioC 2.2 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31432 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 30/04/2008 00:25:58
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5 5 
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Updating the version number for the BioC 2.2 release.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31430 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 29/04/2008 23:50:18
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Fixed bug in LLR2conf, which would fail if all or none calls are hetz

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31391 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/04/2008 16:09:28
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing class nomenclature

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31319 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/04/2008 04:54:06
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5 5 
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minor doc changes to get through check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31313 bc3139a8-67e5-0310-9ffc-ced21a209358

Vince Carey authored on 25/04/2008 00:49:32
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Adding some power user functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@31183 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/04/2008 22:46:08
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Adding support to Affymetrix GeneST Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@30606 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/03/2008 08:53:31
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5 5 
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6 6 
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          splines, RSQLite, preprocessCore, AnnotationDbi,
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10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Fixed problem with readSummaries identifying the wrong number of samples

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29867 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/02/2008 23:15:05
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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Added helper function to read summaries produced by crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29854 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/02/2008 09:12:07
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5 5 
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Removed inconsistent warning given by justCRLMMv2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29616 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/01/2008 14:53:08
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Fixed problem with file that was being closed without even being opened.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29606 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/01/2008 23:48:32
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5 5 
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Unifying CRLMM: 50K, 250K, 5.0 and 6.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29531 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/01/2008 03:35:40
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5 5 
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Some basic methods moved to oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29514 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/01/2008 21:08:20
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5 5 
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Improving support to Affy 5.0 and 6.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@29497 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/01/2008 15:53:18
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5 5 
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Browse code

Fixing docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28222 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/10/2007 14:56:21
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Browse code

Adding support to Affymetrix Tiling arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28162 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/10/2007 15:50:00
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 Package: oligo
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-Version: 1.3.5
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing doc for justCRLMM, which now has tmpdir argment

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28128 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/10/2007 05:03:32
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 Package: oligo
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-Version: 1.3.4
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

1) adding chromosome/position methods for SnpCallSet and friends; 2) pmPosition for SNP is actually pmOffset

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28127 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/10/2007 04:52:37
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 Package: oligo
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-Version: 1.3.3
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Adding PD Info support to Affymetrix Expression Arrays - using db

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28024 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/10/2007 22:37:50
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 Package: oligo
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-Version: 1.3.2
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Adding PD Info support to NimbleGen Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@28003 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/10/2007 19:23:16
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing temp dir

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27825 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/10/2007 03:50:45
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

2nd version bump: bumped y to y+1 in version number x.y.z for all packages in bioc_2.1.manifest (so now y is odd again in trunk).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27716 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 03/10/2007 01:16:39
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

1st version bump: bumped version number x.y.z of all packages in bioc_2.1.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27709 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 03/10/2007 00:41:09
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fix samplenames

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27680 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/10/2007 21:55:06
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

improving justCRLMM output

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27677 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/10/2007 21:30:33
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 Package: oligo
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-Version: 1.1.27
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+Version: 1.1.28
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
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          splines, RSQLite, preprocessCore, AnnotationDbi,
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-         affxparser, oligoClasses
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+         affxparser, oligoClasses (>= 0.99.4)
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 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

- The "db" generic has been renamed "dbconn" in AnnotationDbi so oligo must define the "db" generic itself now. (Note that if this was the only reason to make oligo depend on AnnotationDbi, then maybe this could go away now). - Version bump.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27509 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 25/09/2007 19:16:32
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing code to match docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27414 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/09/2007 03:38:01
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing justCRLMM/justSNPRMA for SNP 6.0 platform

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27344 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/09/2007 15:14:41
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing s4links - docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27271 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/09/2007 13:14:41
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing s4links - docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27270 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/09/2007 12:57:27
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 Package: oligo
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-Version: 1.1.22
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 Title: Oligonucleotide Arrays
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-Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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+Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
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          splines, RSQLite, preprocessCore, AnnotationDbi,
Browse code

fixing vignette and docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27213 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/09/2007 23:05:37
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 LinkingTo: preprocessCore
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-Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
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+Suggests: hapmap100kxba, pd.mapping50k.xba240
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllClasses.R
Browse code

fixed justCRLMM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27200 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/09/2007 17:05:42
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

reducing dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27197 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/09/2007 14:31:33
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 Package: oligo
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

reducing dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@27183 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/09/2007 18:47:36
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 Package: oligo
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-Version: 1.1.17
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+Version: 1.1.19
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.5.9),
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-         splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
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-	 preprocessCore, AnnotationDbi, affxparser, oligoClasses
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+Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58),
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+         splines, RSQLite, preprocessCore, AnnotationDbi,
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+         affxparser, oligoClasses
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 LinkingTo: preprocessCore
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 Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

moving classes to another pkg / fixing docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26919 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/09/2007 04:20:27
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 Package: oligo
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-Version: 1.1.15
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+Version: 1.1.17
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.5.9),
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          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
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-	 preprocessCore, AnnotationDbi, affxparser
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+	 preprocessCore, AnnotationDbi, affxparser, oligoClasses
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
Browse code

Fix crash in affyio due to extra call to fclose

Also updating required version for oligo


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26918 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 07/09/2007 04:14:32
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
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+Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.5.9),
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          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
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 	 preprocessCore, AnnotationDbi, affxparser
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 LinkingTo: preprocessCore
Browse code

bump version for initializer fix

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26917 bc3139a8-67e5-0310-9ffc-ced21a209358

Vince Carey authored on 07/09/2007 03:06:50
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 Package: oligo
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Using normalize.quantiles.use.target for more efficient normalization

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26871 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/09/2007 22:34:34
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Adding a missing file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26544 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/08/2007 03:55:00
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 Package: oligo
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-Version: 1.1.12
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -16,9 +16,9 @@ Collate: AllClasses.R
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          PDInfo-accessors.R
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          methods-platformDesign.R
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          methods-FeatureSet.R
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          methods-TilingFeatureSet.R
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          methods-SnpCallSet.R
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+         methods-SnpCnvFeatureSet.R
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          methods-SnpCopyNumberSet.R
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          read.celfiles.R
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          zzz.R
Browse code

Fixing dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26419 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/08/2007 17:25:50
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 
-	 preprocessCore, AnnotationDbi
8 
+	 preprocessCore, AnnotationDbi, affxparser
9 9 
 LinkingTo: preprocessCore
10 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter, affxparser
10 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllClasses.R
... ... 
@@ -16,6 +16,7 @@ Collate: AllClasses.R
16 16 
          PDInfo-accessors.R
17 17 
          methods-platformDesign.R
18 18 
          methods-FeatureSet.R
19 
+         methods-SnpCnvFeatureSet.R
19 20 
          methods-TilingFeatureSet.R
20 21 
          methods-SnpCallSet.R
21 22 
          methods-SnpCopyNumberSet.R
Browse code

fixing vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26054 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2007 22:58:50
Showing 1 changed files
DESCRIPTION
History View file @ 6b56e8d
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.1.9
2 
+Version: 1.1.10
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

final changes pre-BioC2007

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@26040 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/07/2007 07:18:44
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@@ -1,13 +1,13 @@
1 1 
 Package: oligo
2 
-Version: 1.1.7
2 
+Version: 1.1.9
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 
-	 preprocessCore, affxparser
8 
+	 preprocessCore, AnnotationDbi
9 9 
 LinkingTo: preprocessCore
10 
-Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
10 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter, affxparser
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
12 12 
 License: LGPL version 2 or newer
13 13 
 Collate: AllClasses.R
Browse code

misplaced unlink

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25996 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/07/2007 16:11:43
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1 1 
 Package: oligo
2 
-Version: 1.1.6
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+Version: 1.1.7
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

controlling memory usage

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25981 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/07/2007 17:37:33
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@@ -1,11 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 1.1.5
2 
+Version: 1.1.6
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 
-	 preprocessCore
8 
+	 preprocessCore, affxparser
9 9 
 LinkingTo: preprocessCore
10 10 
 Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
11 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
... ... 
@@ -30,5 +30,7 @@ Collate: AllClasses.R
30 30 
          show-methods.R
31 31 
          snprma.R
32 32 
 	 justSNPRMA.R
33 
+	 justCRLMM.R
34 
+         update.snp6.R
33 35 
 LazyLoad: Yes
34 36 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

adding predicted accuracy to crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25678 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/07/2007 15:28:23
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History View file @ 8bc467d
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@@ -3,7 +3,7 @@ Version: 1.1.5
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: methods, R (>= 2.6.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
6 
+Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 8 
 	 preprocessCore
9 9 
 LinkingTo: preprocessCore
Browse code

bugfix: accessing extdata under Win

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25414 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/06/2007 03:20:27
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1 1 
 Package: oligo
2 
-Version: 1.1.4
2 
+Version: 1.1.5
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

bumping version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25361 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/06/2007 20:11:50
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1 1 
 Package: oligo
2 
-Version: 1.1.2
2 
+Version: 1.1.4
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Trying to fix vignette dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25334 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 12/06/2007 18:30:47
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History View file @ 65ca063
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.1.1
2 
+Version: 1.1.2
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
... ... 
@@ -7,6 +7,7 @@ Depends: methods, R (>= 2.6.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 8 
 	 preprocessCore
9 9 
 LinkingTo: preprocessCore
10 
+Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter
10 11 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
11 12 
 License: LGPL version 2 or newer
12 13 
 Collate: AllClasses.R
Browse code

Require R >= 2.6.0 since const char fixes were made

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25301 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 10/06/2007 17:22:32
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DESCRIPTION
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@@ -3,7 +3,7 @@ Version: 1.1.1
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
6 
+Depends: methods, R (>= 2.6.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 7 
          splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 8 
 	 preprocessCore
9 9 
 LinkingTo: preprocessCore
Browse code

Updatings docs / boxplot+hist ExpressionSet / Fixing version number

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25274 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/06/2007 09:18:34
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 1.0.6
2 
+Version: 1.1.1
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

adding justSNPRMA - less memory intensive / keeping BufferedMatrix only for SNP chips, everything else uses matrix / adding dependence on preprocessCore

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@25042 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/05/2007 06:05:50
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@@ -1,10 +1,12 @@
1 1 
 Package: oligo
2 
-Version: 1.0.5
2 
+Version: 1.0.6
3 3 
 Title: Oligonucleotide Arrays
4 
-Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
4 
+Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarr <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 
-         splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0)
7 
+         splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0),
8 
+	 preprocessCore
9 
+LinkingTo: preprocessCore
8 10 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
9 11 
 License: LGPL version 2 or newer
10 12 
 Collate: AllClasses.R
Browse code

SaveImage is deprecated, using LazyLoad instead

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24616 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 12/05/2007 04:56:41
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@@ -27,5 +27,5 @@ Collate: AllClasses.R
27 27 
          show-methods.R
28 28 
          snprma.R
29 29 
 	 justSNPRMA.R
30 
-SaveImage: Yes
30 
+LazyLoad: Yes
31 31 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Using matrix in assayData. Adding justSNPRMA. Improving performance for SNP chips

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24551 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/05/2007 21:20:40
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1 1 
 Package: oligo
2 
-Version: 1.0.4
2 
+Version: 1.0.5
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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@@ -26,5 +26,6 @@ Collate: AllClasses.R
26 26 
          crlmm.R
27 27 
          show-methods.R
28 28 
          snprma.R
29 
+	 justSNPRMA.R
29 30 
 SaveImage: Yes
30 31 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Fixing featureData on crlmm output / adding example on accessing data via SQL

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24313 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/04/2007 18:24:11
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1 1 
 Package: oligo
2 
-Version: 1.0.3
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+Version: 1.0.4
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Adding vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24299 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/04/2007 02:08:45
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 Package: oligo
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-Version: 1.0.2
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+Version: 1.0.3
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing paths

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24284 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/04/2007 20:51:20
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1 1 
 Package: oligo
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24247 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/04/2007 07:55:20
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1 1 
 Package: oligo
2 
-Version: 1.1.0
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+Version: 1.0.1
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: methods, R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.3.3),
7 
-         splines, RSQLite, BufferedMatrix (>= 0.1.27), BufferedMatrixMethods (>= 0.1.1)
6 
+Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4),
7 
+         splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0)
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
9 9 
 License: LGPL version 2 or newer
10 10 
 Collate: AllClasses.R
Browse code

Bumped again version number x.y.z for all packages in bioc_2.0.manifest (y<-y+1).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24217 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2007 18:31:42
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BioC 2.0 release version bump: bumped version number x.y.z for all packages in bioc_2.0.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@24214 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2007 18:21:48
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

adding suggestion to save memory in computation - to be checked later in the day

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23701 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/04/2007 10:36:40
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

adding geometry method/slot for pdInfoBuilder

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23694 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/04/2007 05:22:26
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

trying to remove the warnings Windows gives on the documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23528 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/03/2007 20:44:09
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

still trying to fix the docs for Windows

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23434 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2007 21:25:40
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing docs links

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23422 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/03/2007 06:21:04
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23405 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/03/2007 20:57:10
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

removing docs warnings

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23372 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/03/2007 21:05:05
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23346 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/03/2007 01:43:33
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23312 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/03/2007 19:12:29
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23303 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/03/2007 23:16:55
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

starting documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23302 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/03/2007 23:14:03
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          methods-SnpCallSet.R
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          methods-SnpCopyNumberSet.R
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          read.celfiles.R
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          zzz.R
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          readxys.R
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Browse code

fix bug in image for SnpFeatureSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23210 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/03/2007 19:07:30
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Generalizing pmSequence for platformDesign objs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23097 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/03/2007 17:03:54
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing problem with image

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23077 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/03/2007 10:43:46
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

cleaning code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@23031 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/03/2007 21:47:40
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

cleaning code, optimizing routines

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22962 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/03/2007 19:31:27
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

removing unecessary things

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22938 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/03/2007 22:37:36
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 Package: oligo
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.3.3),
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-         splines, RSQLite, BufferedMatrix (>= 0.1.27), BufferedMatrixMethods (>=0.1.1)
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+Depends: methods, R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.3.3),
7 
+         splines, RSQLite, BufferedMatrix (>= 0.1.27), BufferedMatrixMethods (>= 0.1.1)
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 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
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 License: LGPL version 2 or newer
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          show-methods.R
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          snprma.R
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 SaveImage: Yes
Browse code

starting doc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22936 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/03/2007 21:07:45
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.3.3),
7 
-         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods,
7 
+         splines, RSQLite, BufferedMatrix (>= 0.1.27), BufferedMatrixMethods (>=0.1.1)
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
9 9 
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          methods-TilingFeatureSet.R
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-         bg.R
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Browse code

Fixing problem to get MM probes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22904 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/03/2007 11:09:44
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing bugs in params update and plots

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22856 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/02/2007 15:26:02
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Browse code

Fixing bugs producing pkgs and reading data for NGS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22743 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/02/2007 21:49:43
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fixing bug in read.celfiles and dependency on affyio

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22641 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/02/2007 04:36:14
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
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+Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.3.3),
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          splines, RSQLite, BufferedMatrix, BufferedMatrixMethods,
8 
-Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
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+Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
9 9 
 License: LGPL version 2 or newer
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 Collate: AllClasses.R
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          AllGenerics.R
Browse code

fix read.celfiles because of changes in affyio

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22640 bc3139a8-67e5-0310-9ffc-ced21a209358

Ben Bolstad authored on 16/02/2007 03:05:47
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fix in read.celfiles

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22632 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/02/2007 04:46:37
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

forgot to bump version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22590 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/02/2007 19:24:23
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

bug fix in read.celfiles / snprma / crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22387 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/02/2007 22:02:40
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
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-         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods, limma, MASS
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+         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods,
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
9 9 
 License: LGPL version 2 or newer
10 10 
 Collate: AllClasses.R
Browse code

fixing dependencies and generics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22190 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/01/2007 20:39:39
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
7 
-         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods, limma
7 
+         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods, limma, MASS
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
9 9 
 License: LGPL version 2 or newer
10 10 
 Collate: AllClasses.R
Browse code

Bug fixes in CRLMM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22168 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/01/2007 17:08:53
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

minor fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@22030 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/01/2007 18:54:19
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
7 
-         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods
6 
+Depends: R (>= 2.5.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
7 
+         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods, limma
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
9 9 
 License: LGPL version 2 or newer
10 10 
 Collate: AllClasses.R
Browse code

changing the codes to handle SQL

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21952 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/01/2007 06:25:32
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2 
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 Title: Oligonucleotide Arrays
4 4 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

bug fix: snprma for platformDesign objs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21856 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/01/2007 07:49:57
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

adding snprma to collate

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21836 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/01/2007 04:43:22
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5 5 
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30 30 
          crlmm.R
31 31 
          methods-SnpCallSetPlus.R
32 32 
          show-methods.R
33 
+         snprma.R
33 34 
 SaveImage: Yes
34 35 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

organizing code for snprma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21825 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/01/2007 22:00:44
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4 4 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Removing unnecessary code and fixing access to SQL

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21815 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/01/2007 01:12:44
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

minor bugfixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21735 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/01/2007 15:59:19
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Modifications by Benilton Week: Dec/25 - Dec/29

Many modifications to get CRLMM working on the 500K set via SQL data pkgs.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21697 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/12/2006 07:09:58
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 Title: Oligonucleotide Arrays
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
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19 19 
          bg.R
20 20 
          normalize.quantiles.R
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          read.celfiles.R
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23 22 
          rma.R
24 
-         rma2.R
25 23 
          zzz.R
26 24 
          plotDensity.R
27 25 
          readxys.R
Browse code

Added dependencies: BufferedMatrix, BufferedMatrixMethods

Added capabilities to use BufferedMatrix objects in assayData
of *FeatureSet objects (only for Affymetrix right now).

Added read.celfiles2() and rma2(): these functions work directly
with BufferedMatrix objects, saving memory. My goal is to
replace the current functions by these. Already tested and validated.

Modified pm(), so it returns a BufferedMatrix. This allows the use of
rma2().

Changed rma(), so it coerces the result of pm() to matrix.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21629 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/12/2006 09:27:12
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1 1 
 Package: oligo
2 
-Version: 0.99.42
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+Version: 0.99.43
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
7 
-         splines, RSQLite
7 
+         splines, RSQLite, BufferedMatrix, BufferedMatrixMethods
8 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
9 9 
 License: LGPL version 2 or newer
10 10 
 Collate: AllClasses.R
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@@ -19,7 +19,9 @@ Collate: AllClasses.R
19 19 
          bg.R
20 20 
          normalize.quantiles.R
21 21 
          read.celfiles.R
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22 23 
          rma.R
24 
+         rma2.R
23 25 
          zzz.R
24 26 
          plotDensity.R
25 27 
          readxys.R
Browse code

Add probeNames and geneNames methods, fixup rma()

Working towards being able to call rma on a feature set based
on SQLite PDInfo. These methods need new names!


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21611 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 20/12/2006 23:45:59
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 Package: oligo
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-Version: 0.99.41
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Add tableInfo slot to DBPDInfo and an initialize method to fill it

For now, the tableInfo slot is a data.frame that
contains meta data about tables in the DB. For now, we just cache
a copy of the DB's table_info table which has row counts for all
tables.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21560 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 19/12/2006 00:09:10
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Start to add accessor methods for AffySNPPDInfo class

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21511 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 16/12/2006 00:37:09
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1 1 
 Package: oligo
2 
-Version: 0.99.39
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+Version: 0.99.40
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8), splines
6 
+Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8),
7 
+         splines, RSQLite
7 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 9 
 License: LGPL version 2 or newer
9 10 
 Collate: AllClasses.R
10 11 
          AllGenerics.R
11 12 
          basecontent.R
13 
+         PDInfo-accessors.R
12 14 
          methods-platformDesign.R
13 15 
          methods-FeatureSet.R
14 16 
          methods-TilingFeatureSet.R
Browse code

Move show methods to show-methods.R

platformDesign show method now makes use of superclass's
show method.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21506 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 15/12/2006 22:37:34
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1 1 
 Package: oligo
2 
-Version: 0.99.38
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+Version: 0.99.39
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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27 27 
          methods-SnpFeatureSet.R
28 28 
          crlmm.R
29 29 
          methods-SnpCallSetPlus.R
30 
+         show-methods.R
30 31 
 SaveImage: Yes
31 32 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Move all setGeneric calls to AllGenerics.R

Also removed all conditional setGeneric calls, either we
want to define a generic or define methods for a generic that
we know about. No sense in if(is.null(getGeneric(...))).


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21504 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 15/12/2006 22:37:32
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1 1 
 Package: oligo
2 
-Version: 0.99.37
2 
+Version: 0.99.38
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8), splines
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R methods-SnpCallSetPlus.R
9 
+Collate: AllClasses.R
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+         AllGenerics.R
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+         basecontent.R
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+         methods-platformDesign.R
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+         methods-FeatureSet.R
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+         methods-TilingFeatureSet.R
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+         methods-SnpCallSet.R
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+         methods-SnpCopyNumberSet.R
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+         bg.R
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+         normalize.quantiles.R
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+         read.celfiles.R
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+         rma.R
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+         zzz.R
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+         plotDensity.R
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+         readxys.R
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+         sequence.R
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+         utils.R
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+         methods-SnpQSet.R
27 
+         methods-SnpFeatureSet.R
28 
+         crlmm.R
29 
+         methods-SnpCallSetPlus.R
10 30 
 SaveImage: Yes
11 31 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: Many fixes and improvements.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@21475 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 13/12/2006 06:45:22
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 Package: oligo
2 
-Version: 0.99.29
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+Version: 0.99.37
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Adding features for Exon Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20968 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/11/2006 05:15:49
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: fixing DESCRIPTION

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20780 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 23/10/2006 16:57:44
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 Package: oligo
2 
-Version: 0.99.27
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+Version: 0.99.28
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8), splines
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R methods-SnpCallSetPlus.R
9 
+Collate: AllClasses.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R methods-SnpCallSetPlus.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: Oct 18, 2006 - cleaning code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20686 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/10/2006 14:08:19
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-Version: 0.99.26
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Fix invalid regular expressions: "\." => "\\."

R-2.5 gives a warning when it encounters unknown escapes. To
match "." in a regex and not have a warning, use "\\." in the
pattern.

Maintainers: please review for correct behavior.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20628 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 17/10/2006 17:47:13
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Oct 12 - Adding sampleName as default title in imageNGS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20532 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 12/10/2006 14:44:53
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: fixing storageMode

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20515 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/10/2006 21:06:36
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4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Oct 11, 2006 - BC: fixing bottleneck in oligo and a bug for NGS parser in makePlatformDesign

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20514 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/10/2006 20:41:30
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Oct 3: BC - fixing full path problem for CEL files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20360 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/10/2006 15:09:08
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 Package: oligo
2 
-Version: 0.99.21
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+Version: 0.99.22
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fixing NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20355 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/10/2006 06:07:46
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 Package: oligo
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-Version: 0.99.20
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+Version: 0.99.21
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Sept 29, 2006 - Adding NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@20266 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/09/2006 02:47:01
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1 1 
 Package: oligo
2 
-Version: 0.99.19
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+Version: 0.99.20
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.3.0), Biobase (>= 1.11.30), affyio (>= 1.1.8), splines
6 
+Depends: R (>= 2.4.0), Biobase (>= 1.11.42), affyio (>= 1.1.8), splines
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R methods-SnpCallSetPlus.R
Browse code

BC: implementing some details for SNP arrays and fixing minor bugs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19841 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/09/2006 05:29:12
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1 1 
 Package: oligo
2 
-Version: 0.99.18
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+Version: 0.99.19
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC 09/08/06 - minor bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19701 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/09/2006 20:45:30
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 Depends: R (>= 2.3.0), Biobase (>= 1.11.30), affyio (>= 1.1.8), splines
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R methods-SnpCallSetPlus.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: 09/04/06 implementing crlmm & new classes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19612 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/09/2006 14:30:00
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@@ -3,8 +3,7 @@ Version: 0.99.18
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.3.0), Biobase (>= 1.11.30), affyio (>= 1.1.8)
7 
-Suggests: splines
6 
+Depends: R (>= 2.3.0), Biobase (>= 1.11.30), affyio (>= 1.1.8), splines
8 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
9 8 
 License: LGPL version 2 or newer
10 9 
 Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R
Browse code

BC: Aug 30, 2006 - optimizing use of memory

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19526 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/08/2006 19:18:06
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1 1 
 Package: oligo
2 
-Version: 0.99.17
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+Version: 0.99.18
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
6 
+Depends: R (>= 2.3.0), Biobase (>= 1.11.30), affyio (>= 1.1.8)
7 
+Suggests: splines
7 8 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 9 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R methods-SnpFeatureSet.R crlmm.R
10 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R methods-SnpCallSet.R methods-SnpCopyNumberSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R methods-SnpQSet.R methods-SnpFeatureSet.R crlmm.R
10 11 
 SaveImage: Yes
11 12 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: changing some approaches to run the 500K

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19257 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/08/2006 15:12:42
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 Package: oligo
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-Version: 0.99.16
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+Version: 0.99.17
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

little updates for crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@19055 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/08/2006 14:06:10
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 Package: oligo
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-Version: 0.99.15
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+Version: 0.99.16
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

adding crlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18901 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/07/2006 19:35:16
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@@ -6,6 +6,6 @@ Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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 Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R methods-SnpFeatureSet.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R methods-SnpFeatureSet.R crlmm.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: July 6, 2006 - adding methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18759 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/07/2006 17:32:57
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1 1 
 Package: oligo
2 
-Version: 0.99.14
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+Version: 0.99.15
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R methods-SnpFeatureSet.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: Jul 1, 2006 - adding getM, getA, renaming to snprma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18679 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/07/2006 19:32:40
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 Package: oligo
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-Version: 0.99.13
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+Version: 0.99.14
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jun 28, 2006 - adding SnpQSet class

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18638 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/06/2006 06:09:22
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1 1 
 Package: oligo
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-Version: 0.99.12
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+Version: 0.99.13
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
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+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R funcs4qset.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

fix qnorm.c code so builds on sparc solaris (or at least hope that it does)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18392 bc3139a8-67e5-0310-9ffc-ced21a209358

Ben Bolstad authored on 09/06/2006 21:40:12
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 Package: oligo
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-Version: 0.99.11
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

resync qnorm.c code with other packages where it appears.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18379 bc3139a8-67e5-0310-9ffc-ced21a209358

Ben Bolstad authored on 08/06/2006 23:44:12
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 Package: oligo
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-Version: 0.99.10
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: May 16, 2006 - bugfix (validation)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@18131 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/05/2006 21:58:50
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 Package: oligo
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-Version: 0.99.8
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+Version: 0.99.10
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: fixes for Tiling Arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17934 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/05/2006 23:29:07
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 Package: oligo
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-Version: 0.99.7
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+Version: 0.99.8
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: bugfix for XYS parser

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17823 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 30/04/2006 20:56:26
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 Package: oligo
2 
-Version: 0.99.6
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+Version: 0.99.7
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: fixing bugs for tiling arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17665 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/04/2006 20:34:02
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1 1 
 Package: oligo
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-Version: 0.99.5
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+Version: 0.99.6
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R methods-TilingFeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: fixing bugs for tiling arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17663 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 24/04/2006 19:46:05
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 Package: oligo
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-Version: 0.99.4
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+Version: 0.99.5
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.3.0), Biobase (>= 1.9.18), affyio
6 
+Depends: R (>= 2.3.0), Biobase (>= 1.9.28), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
Browse code

BC: fixing initialize method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17547 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 21/04/2006 18:30:22
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 Package: oligo
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 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: fixing more things broken by the new eSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17337 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/04/2006 23:10:45
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DESCRIPTION
History View file @ 4b71d1f
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1 1 
 Package: oligo
2 
-Version: 0.99.2
2 
+Version: 0.99.3
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.3.0), Biobase (>= 1.9.18), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-FeatureSet.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

BC: Fixing oligo and makePlatformDesign to work with the new eSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17305 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 18/04/2006 06:52:23
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DESCRIPTION
History View file @ aaae2cf
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1 1 
 Package: oligo
2 
-Version: 0.99.0
2 
+Version: 0.99.2
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.6), affyio
6 
+Depends: R (>= 2.3.0), Biobase (>= 1.9.18), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
Browse code

Fixing documentation for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17095 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/04/2006 21:13:39
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DESCRIPTION
History View file @ 1cd0066
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 0.5.3
2 
+Version: 0.99.0
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Apr 6, 2006: BC - fixing problems with the documentation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@17057 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 06/04/2006 16:57:11
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DESCRIPTION
History View file @ 26fce1b
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 0.5.2
2 
+Version: 0.5.3
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Apr 3, 2006 - added basecontent from matchprobes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16990 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/04/2006 13:10:39
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DESCRIPTION
History View file @ cab3b89
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@@ -1,11 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 0.5.1
2 
+Version: 0.5.2
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6), affyio
7 7 
 Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
9 
+Collate: AllClasses.R AllGeneric.R basecontent.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Mar 28, 2006: BC - minor changes and initial version of documentation.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16883 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/03/2006 23:12:15
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History View file @ d72eef4
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1 1 
 Package: oligo
2 
-Version: 0.5.0
2 
+Version: 0.5.1
3 3 
 Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Minor corrections on the Description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16688 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/03/2006 15:00:29
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DESCRIPTION
History View file @ 138bdc1
... ... 
@@ -8,4 +8,4 @@ Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling)
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 
-biocViews: OneChannel,Microarray,Preprocessing
11 
+biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Browse code

Minor corrections on the Description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16682 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/03/2006 06:31:00
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DESCRIPTION
History View file @ 5994f32
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@@ -1,10 +1,10 @@
1 1 
 Package: oligo
2 
-Version: 0.4.9
3 
-Title: Gene Expression Analysis
2 
+Version: 0.5.0
3 
+Title: Oligonucleotide Arrays
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6), affyio
7 
-Description: A package to analyze gene expression data.
7 
+Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling) at probe-level.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
Browse code

Mar 13, 2006: BC - adding BPMAP capabilities to oligo/makePlatformDesign - oligo handles Affy tiling arrays (initial version)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16609 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/03/2006 00:30:28
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History View file @ 3ca7700
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 0.4.8
2 
+Version: 0.4.9
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: minor changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16436 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/03/2006 04:18:51
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History View file @ 9214b21
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1 1 
 Package: oligo
2 
-Version: 0.4.7
2 
+Version: 0.4.8
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Feb 28, 2006 - added dependence on affyio. restored the assignments of classes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16416 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 01/03/2006 03:18:16
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History View file @ 0efdc37
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@@ -1,9 +1,9 @@
1 1 
 Package: oligo
2 
-Version: 0.4.6
2 
+Version: 0.4.7
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.6)
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.6), affyio
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
Browse code

BC: Feb 26, 2006 - fixing bug in normalize.quantiles

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16370 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/02/2006 18:50:31
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@@ -1,5 +1,5 @@
1 1 
 Package: oligo
2 
-Version: 0.4.5
2 
+Version: 0.4.6
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Feb 25, 2006 - some fixes on image() and boxplot()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@16363 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/02/2006 23:18:00
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1 1 
 Package: oligo
2 
-Version: 0.4.4
2 
+Version: 0.4.5
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

RI: added bg.correct.rma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15906 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 26/01/2006 20:41:01
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@@ -1,11 +1,11 @@
1 1 
 Package: oligo
2 
-Version: 0.4.3
2 
+Version: 0.4.4
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6)
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
9 
+Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R bg.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 11 
 biocViews: OneChannel,Microarray,Preprocessing
Browse code

BC: Jan 26, 2006 - fixing pm<- mm<-

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15898 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 26/01/2006 17:16:22
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1 1 
 Package: oligo
2 
-Version: 0.4.2
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+Version: 0.4.3
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 15, 2006 - bug fix: rownames in exprs() were in the wrong order (CEL files only)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15740 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/01/2006 22:31:56
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1 1 
 Package: oligo
2 
-Version: 0.4.1
2 
+Version: 0.4.2
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 10, 2006 - power-user features added.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15669 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/01/2006 23:53:43
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1 1 
 Package: oligo
2 
-Version: 0.4.0
2 
+Version: 0.4.1
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 10, 2006 - Added features to read SD and NPIXELS from CEL files.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15650 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/01/2006 07:33:38
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1 1 
 Package: oligo
2 
-Version: 0.3.9
2 
+Version: 0.4.0
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 8, 2006 - PDEnvs are optionally loaded for Affy chips

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15615 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/01/2006 18:13:25
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1 1 
 Package: oligo
2 
-Version: 0.3.8
2 
+Version: 0.3.9
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 05, 2005 - forgot to bump version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15573 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 05/01/2006 05:37:31
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1 1 
 Package: oligo
2 
-Version: 0.3.7
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+Version: 0.3.8
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Jan 02, 2005 - improving the structure of the package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15552 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/01/2006 01:06:39
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1 1 
 Package: oligo
2 
-Version: 0.3.6
2 
+Version: 0.3.7
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6)
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R indextools.R
9 
+Collate: AllClasses.R AllGeneric.R methods-platformDesign.R methods-oligoBatch.R normalize.quantiles.R read.celfiles.R rma.R zzz.R plotDensity.R readxys.R sequence.R utils.R
10 10 
 SaveImage: Yes
11 
-biocViews: OneChannel,Microarray,Preprocessing
12 11 
\ No newline at end of file
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+biocViews: OneChannel,Microarray,Preprocessing
Browse code

BC: Dec 17, 2005 - bug corrections for NG data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15439 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 17/12/2005 20:44:52
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1 1 
 Package: oligo
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-Version: 0.3.5
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+Version: 0.3.6
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Dec 9, 2005 - changing variable names and a some things that depended on them

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15304 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/12/2005 01:38:58
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1 1 
 Package: oligo
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-Version: 0.3.3
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Dec 8, 2005: Fixing multi-well readings - NG

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@15288 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/12/2005 00:42:20
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: 16 Nov 2005 - changes in some methods to adapt to the new order in PDenv - added i2xy and xy2i

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14922 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/11/2005 21:49:51
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1 1 
 Package: oligo
2 
-Version: 0.3.1
2 
+Version: 0.3.2
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6)
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
9 
+Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R indextools.R
10 10 
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\ No newline at end of file
Browse code

BC: Nov 8, 2005 - bugfix in readxys

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14757 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/11/2005 15:02:11
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1 1 
 Package: oligo
2 
-Version: 0.3.0
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+Version: 0.3.1
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
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8 8 
 License: LGPL version 2 or newer
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 Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
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Browse code

Version bump to begin bioc 1.8 devel track.

Redone after a first attempt got it wrong.
All packages should have x.y.z with y odd for devel.
For details on the version number schedule, please see:
http://bioconductor.fhcrc.org/developers/devwiki/VersionNumberingStandards



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14473 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 12/10/2005 23:58:15
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-Version: 0.1.1
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+Version: 0.3.0
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Revert version bump that was incorrectly done. Will try again in a bit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14472 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 12/10/2005 23:35:06
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-Version: 0.2.0
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

Version bump to begin Bioc 1.8 DEVEL work.

This version bump is unusual in that it is part of a catch-up version bump.
The project has decided to work with an even/odd scheme.

All versions are x.y.z.
In release y is even.
In devel y is odd.

This change sets everyone to the next odd y (next as compared to
version in 1.7 release).


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14469 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 12/10/2005 20:42:18
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-Version: 0.1.1
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Sept 27, 2005 - Bug fix: NimbleGen

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14272 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/09/2005 20:10:27
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1 1 
 Package: oligo
2 
-Version: 0.1.0
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
10 10 
 SaveImage: Yes
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Browse code

Move note() into Biobase

The less severe warning() func note() was in reposTools and affy and oligo
depended on reposTools just for this function. Moved a copy of note()
into Biobase and removed the reposTools dependencies.




git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@14243 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 25/09/2005 20:34:33
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@@ -3,7 +3,7 @@ Version: 0.1.0
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.6), reposTools
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.6)
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
Browse code

RI: change to rma2.c to avoid segfault

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13900 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 03/09/2005 18:17:10
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1 1 
 Package: oligo
2 
-Version: 0.0.9
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+Version: 0.1.0
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Aug 29, 2005 - Modified show()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13766 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 29/08/2005 15:56:13
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 Title: Gene Expression Analysis
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

RI: added quantile normalization for oligoBatch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13655 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 22/08/2005 14:40:23
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6 6 
 Depends: R (>= 2.2.0), Biobase (>= 1.6.6), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
9 
+Collate: oligoBatch.R boxplot.R image.R normalize.quantiles.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
10 10 
 SaveImage: Yes
Browse code

RI: added quantile normalization for oligoBatch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13654 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 22/08/2005 14:34:48
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 Package: oligo
2 
-Version: 0.0.7
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

fix endian issues in source code. Note that this should have absolutely no effect on either little or big endian systems for reading of cel files, but makes the code more correct.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13619 bc3139a8-67e5-0310-9ffc-ced21a209358

Ben Bolstad authored on 17/08/2005 04:03:09
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1 1 
 Package: oligo
2 
-Version: 0.0.6
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+Version: 0.0.7
3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Setting depend. to Biobase 1.6.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13479 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/08/2005 16:35:37
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3 3 
 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.5), reposTools
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.6), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
Browse code

BC: Setting depend. to Biobase 1.6.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13478 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/08/2005 16:33:25
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 Title: Gene Expression Analysis
4 4 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.4), reposTools
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.5), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
Browse code

RI: changed .Data to eList

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13477 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 04/08/2005 16:28:06
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1 1 
 Package: oligo
2 
-Version: 0.0.5
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Fixing dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13475 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/08/2005 16:07:11
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3 3 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.5), reposTools
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.4), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
Browse code

BC: Aug 02, 2005 - Fixing Dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13452 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/08/2005 18:56:14
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@@ -3,7 +3,7 @@ Version: 0.0.5
3 3 
 Title: Gene Expression Analysis
4 4 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
6 
-Depends: R (>= 2.2.0), Biobase (>= 1.6.4), reposTools
6 
+Depends: R (>= 2.2.0), Biobase (>= 1.6.5), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
Browse code

BC: Aug 02, 2005 - Updating Version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13448 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/08/2005 16:53:41
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 Package: oligo
2 
-Version: 0.0.4
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+Version: 0.0.5
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

BC: Thu, Jul 28, 2005 - pm/mm returns identifies as rownames if genenames is given; pm and mm methods have exclusive files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13411 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/07/2005 23:43:07
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 Depends: R (>= 2.2.0), Biobase (>= 1.6.4), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
-Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R
9 
+Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R pm.R mm.R
10 10 
 SaveImage: Yes
Browse code

BC: Th, Jul 28, 2005 - correcting dependencies: Biobase 1.6.4 and R 2.2.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13408 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/07/2005 19:35:32
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3 3 
 Title: Gene Expression Analysis
4 4 
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5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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-Depends: R (>= 2.1.0), Biobase (>= 1.6.2), reposTools
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+Depends: R (>= 2.2.0), Biobase (>= 1.6.4), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 9 
 Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R
Browse code

BC: Th, Jul 28, 2005 - added description slot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13407 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/07/2005 19:32:41
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 Depends: R (>= 2.1.0), Biobase (>= 1.6.2), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
+Collate: oligoBatch.R boxplot.R image.R platformDesign.R read.celfiles.R rma.R zzz.R featureIndex.R plotDensity.R readxys.R sequence.R
9 10 
 SaveImage: Yes
Browse code

RI: fixed DESCRIPTION to avoid error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13392 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 28/07/2005 00:38:03
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 Depends: R (>= 2.1.0), Biobase (>= 1.6.2), reposTools
7 7 
 Description: A package to analyze gene expression data.
8 8 
 License: LGPL version 2 or newer
9 
+SaveImage: Yes
Browse code

RI: changed DESCRIPTION to require Biobase.. uped the version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@13253 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 19/07/2005 18:20:28
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1 1 
 Package: oligo
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 Title: Gene Expression Analysis
4 4 
 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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+Depends: R (>= 2.1.0), Biobase (>= 1.6.2), reposTools
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 Description: A package to analyze gene expression data.
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 License: LGPL version 2 or newer
Browse code

RI: many changes to oligo. including changing names of files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@12520 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 20/05/2005 15:39:27
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 Package: oligo
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-Version: 0.0.2
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+Version: 0.0.3
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 Title: Gene Expression Analysis
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 Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
5 5 
 Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
Browse code

RI: oligo package is being added. It will cover affy expression and snp as well as nimblegen arrays

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@11917 bc3139a8-67e5-0310-9ffc-ced21a209358

Rafael Irizarry authored on 21/04/2005 15:39:25
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+Package: oligo
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+Version: 0.0.2
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+Title: Gene Expression Analysis
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+Author: Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber
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+Maintainer: Benilton Carvalho <bcarvalh@jhsph.edu>
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+Description: A package to analyze gene expression data.
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+License: LGPL version 2 or newer