git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44968 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -386,7 +386,7 @@ is stored in the assayData slot. |
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2010-02-07 B. Carvalho - committed version 1.5.25 |
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* Updated requirement of affyio to support Win64 |
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-2010-02-20 R. Scharpf - committed version 1.5.25 |
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+2010-02-20 R. Scharpf - committed version 1.5.26 |
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** begin adding support for ff |
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@@ -400,8 +400,13 @@ is stored in the assayData slot. |
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- B.rda |
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- cn_rmaResult.rda (SKW) |
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-2010-02-21 R. Scharpf - committed version 1.5.26 |
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+2010-02-21 R. Scharpf - committed version 1.5.27 |
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** additional support for ff in crlmm and computeCopynumber functions |
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- |
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+2010-03-02 M. Ritchie - committed version 1.5.28 |
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+ * Added message to readIDAT() warning that older style IDAT files can not be read in. |
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+Such files arise when scanner settings contain the line <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles> |
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+If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, |
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+then readIDAT() should work. Thanks to Pierre Cherel who reported this error. |
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+ * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build) |
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@@ -1,8 +1,8 @@ |
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Package: crlmm |
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Type: Package |
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Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
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-Version: 1.5.27 |
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-Date: 2010-02-21 |
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+Version: 1.5.28 |
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+Date: 2010-03-02 |
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Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au> |
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Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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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 |
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@@ -27,8 +27,7 @@ Suggests: hapmapsnp5, |
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genomewidesnp6Crlmm (>= 1.0.2), |
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snpMatrix, |
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metaArray |
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-Collate: AllClasses.R |
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- AllGenerics.R |
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+Collate: AllGenerics.R |
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methods-CNSet.R |
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methods-eSet.R |
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methods-SnpSuperSet.R |
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@@ -190,6 +190,9 @@ readIDAT <- function(idatFile){ |
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versionNumber <- readBin(tempCon, "integer", n=1, size=8, |
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endian="little", signed=FALSE) |
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+ |
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+ if(versionNumber<3) |
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+ stop("Older style IDAT files not supported: consider updating your scanner settings") |
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nFields <- readBin(tempCon, "integer", n=1, size=4, |
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endian="little", signed=FALSE) |