deleted file mode 100644

@@ -1,51 +0,0 @@

-        **************************************************

-        *                                                *

-        *              1.3 SERIES NEWS                   *

-        *                                                *

-        **************************************************

-

-USER VISIBLE CHANGES

-

-     o 3 new classes created:

-

-        i.  'ABset': container for quantile-normalized A and B

-       	    intensities for both SNP and copy number probes.  Required

-       	    assay data elements are 'A' and 'B'.  Extends eSet

-       	    directly.

-

-                - For nonpolymorphic probes, the quantile normalized

-                  intensity is stored in the 'A' assay data element.

-                  The corresponding row in the 'B' assay data element

-                  is NA.  This is a bit inefficient, but greatly

-                  simplifies downstream analyses.  In particular, '['

-                  works.

-

-        ii.  'CrlmmSetList': container for results from preprocessing

-	     and genotyping.  This object is a list.  The first

-	     element of the list is an ABset.  The second element is a

-	     SnpSet containing genotype calls.  The two elements are

-	     required to have identical featureNames and sampleNames.

-

-       		- added several methods for subsetting and accessing

- 		  elements of this object, including featureNames,

- 		  sampleNames, and "[".

-

-         iii. 'CopyNumberSet': contains locus-level estimates of copy

-  	      number for SNPs and polymorphic probes.

-

-       	        - Required assay data elements are 'CA' and 'CB',

-                  corresponding to the absolute copy number for allele

-                  A and B, respectively.

-

-	        - For nonpolymorphic probes, the total copy number is

-                  stored in the 'CA' slot and a NA is recorded for the

-                  corresponding row in the CB matrix. 

-

-		- Useful methods: 'copyNumber', 'ellipse', 'points'

-

-     o 'crlmmWrapper' function does preprocessing

-       (quantile-normalization) and genotyping, saving an object of

-       class CrlmmSetList for each chromosome

-

-     o 'computeCopynumber' now requires an object of class

-        'CrlmmSetList' and returns an object of class 'CopyNumberSet'.

@@ -1,17 +1,3 @@

-        **************************************************

-        *                                                *

-        *              1.5 SERIES NEWS                   *

-        *                                                *

-        **************************************************

-

-USER VISIBLE CHANGES

-

-NEW FEATURES

-

-	o Support to large datasets via ff package. The user

-	must load the ff package manually to benefit from

-	this.

-

         **************************************************

         *                                                *

         *              1.3 SERIES NEWS                   *

@@ -1,3 +1,17 @@

+        **************************************************

+        *                                                *

+        *              1.5 SERIES NEWS                   *

+        *                                                *

+        **************************************************

+

+USER VISIBLE CHANGES

+

+NEW FEATURES

+

+	o Support to large datasets via ff package. The user

+	must load the ff package manually to benefit from

+	this.

+

         **************************************************

         *                                                *

         *              1.3 SERIES NEWS                   *

new file mode 100644

@@ -0,0 +1,51 @@

+        **************************************************

+        *                                                *

+        *              1.3 SERIES NEWS                   *

+        *                                                *

+        **************************************************

+

+USER VISIBLE CHANGES

+

+     o 3 new classes created:

+

+        i.  'ABset': container for quantile-normalized A and B

+       	    intensities for both SNP and copy number probes.  Required

+       	    assay data elements are 'A' and 'B'.  Extends eSet

+       	    directly.

+

+                - For nonpolymorphic probes, the quantile normalized

+                  intensity is stored in the 'A' assay data element.

+                  The corresponding row in the 'B' assay data element

+                  is NA.  This is a bit inefficient, but greatly

+                  simplifies downstream analyses.  In particular, '['

+                  works.

+

+        ii.  'CrlmmSetList': container for results from preprocessing

+	     and genotyping.  This object is a list.  The first

+	     element of the list is an ABset.  The second element is a

+	     SnpSet containing genotype calls.  The two elements are

+	     required to have identical featureNames and sampleNames.

+

+       		- added several methods for subsetting and accessing

+ 		  elements of this object, including featureNames,

+ 		  sampleNames, and "[".

+

+         iii. 'CopyNumberSet': contains locus-level estimates of copy

+  	      number for SNPs and polymorphic probes.

+

+       	        - Required assay data elements are 'CA' and 'CB',

+                  corresponding to the absolute copy number for allele

+                  A and B, respectively.

+

+	        - For nonpolymorphic probes, the total copy number is

+                  stored in the 'CA' slot and a NA is recorded for the

+                  corresponding row in the CB matrix. 

+

+		- Useful methods: 'copyNumber', 'ellipse', 'points'

+

+     o 'crlmmWrapper' function does preprocessing

+       (quantile-normalization) and genotyping, saving an object of

+       class CrlmmSetList for each chromosome

+

+     o 'computeCopynumber' now requires an object of class

+        'CrlmmSetList' and returns an object of class 'CopyNumberSet'.