@@ -386,7 +386,7 @@ is stored in the assayData slot.

 2010-02-07 B. Carvalho - committed version 1.5.25

  * Updated requirement of affyio to support Win64

-2010-02-20 R. Scharpf - committed version 1.5.25

+2010-02-20 R. Scharpf - committed version 1.5.26

 ** begin adding support for ff

@@ -400,8 +400,13 @@ is stored in the assayData slot.

       - B.rda

       - cn_rmaResult.rda (SKW)

-2010-02-21 R. Scharpf - committed version 1.5.26

+2010-02-21 R. Scharpf - committed version 1.5.27

 ** additional support for ff in crlmm and computeCopynumber functions

-

+2010-03-02 M. Ritchie - committed version 1.5.28

+ * Added message to readIDAT() warning that older style IDAT files can not be read in.

+Such files arise when scanner settings contain the line <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles>

+If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 

+then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

+ * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)

@@ -1,8 +1,8 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.5.27

-Date: 2010-02-21

+Version: 1.5.28

+Date: 2010-03-02

 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 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,

           genomewidesnp6Crlmm (>= 1.0.2),

           snpMatrix,

           metaArray

-Collate: AllClasses.R

-	 AllGenerics.R

+Collate: AllGenerics.R

 	 methods-CNSet.R

 	 methods-eSet.R

          methods-SnpSuperSet.R

@@ -190,6 +190,9 @@ readIDAT <- function(idatFile){

   versionNumber <- readBin(tempCon, "integer", n=1, size=8, 

                            endian="little", signed=FALSE)

+

+  if(versionNumber<3)

+    stop("Older style IDAT files not supported:  consider updating your scanner settings")

   nFields <- readBin(tempCon, "integer", n=1, size=4, 

                      endian="little", signed=FALSE)