git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44968 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 02/03/2010 05:33:50
Showing 3 changed files

... ...
@@ -386,7 +386,7 @@ is stored in the assayData slot.
386 386
 2010-02-07 B. Carvalho - committed version 1.5.25
387 387
  * Updated requirement of affyio to support Win64
388 388
 
389
-2010-02-20 R. Scharpf - committed version 1.5.25
389
+2010-02-20 R. Scharpf - committed version 1.5.26
390 390
 
391 391
 ** begin adding support for ff
392 392
 
... ...
@@ -400,8 +400,13 @@ is stored in the assayData slot.
400 400
       - B.rda
401 401
       - cn_rmaResult.rda (SKW)
402 402
 
403
-2010-02-21 R. Scharpf - committed version 1.5.26
403
+2010-02-21 R. Scharpf - committed version 1.5.27
404 404
  
405 405
 ** additional support for ff in crlmm and computeCopynumber functions
406 406
 
407
-
407
+2010-03-02 M. Ritchie - committed version 1.5.28
408
+ * Added message to readIDAT() warning that older style IDAT files can not be read in.
409
+Such files arise when scanner settings contain the line <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles>
410
+If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 
411
+then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
412
+ * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)
... ...
@@ -1,8 +1,8 @@
1 1
 Package: crlmm
2 2
 Type: Package
3 3
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4
-Version: 1.5.27
5
-Date: 2010-02-21
4
+Version: 1.5.28
5
+Date: 2010-03-02
6 6
 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
7 7
 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ...
@@ -27,8 +27,7 @@ Suggests: hapmapsnp5,
27 27
           genomewidesnp6Crlmm (>= 1.0.2),
28 28
           snpMatrix,
29 29
           metaArray
30
-Collate: AllClasses.R
31
-	 AllGenerics.R
30
+Collate: AllGenerics.R
32 31
 	 methods-CNSet.R
33 32
 	 methods-eSet.R
34 33
          methods-SnpSuperSet.R
... ...
@@ -190,6 +190,9 @@ readIDAT <- function(idatFile){
190 190
 
191 191
   versionNumber <- readBin(tempCon, "integer", n=1, size=8, 
192 192
                            endian="little", signed=FALSE)
193
+
194
+  if(versionNumber<3)
195
+    stop("Older style IDAT files not supported:  consider updating your scanner settings")
193 196
   
194 197
   nFields <- readBin(tempCon, "integer", n=1, size=4, 
195 198
                      endian="little", signed=FALSE)