@@ -303,5 +303,8 @@ is decoded and scanned

  * updated illumina_copynumber vignette

+2009-10-25 M Ritchie - committed version 1.3.24

+ * fixed bug in readIdatFiles()

+ * updated crlmmIllumina.Rnw and crlmmIllumina.pdf

@@ -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: 1.3.23

-Date: 2009-09-29

+Version: 1.3.24

+Date: 2009-10-25

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, 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 6.0.

@@ -12,14 +12,18 @@ readIdatFiles <- function(sampleSheet=NULL,

 			  sep="_",

 			  fileExt=list(green="Grn.idat", red="Red.idat"),

 			  saveDate=FALSE) {

-       if(is.null(arrayNames)) {

-	       arrayNames = gsub(paste(sep, fileExt$green, sep=""), "", dir(pattern=fileExt$green, path=path))

-	       if(!is.null(sampleSheet)) {

-		       sampleSheet=NULL

-		       cat("Could not find required info in \'sampleSheet\' - ignoring.  Check \'sampleSheet\' and/or \'arrayInfoColNames\'\n")

-	       }

-	       pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

-       }	

+#       if(!is.null(arrayNames)) {

+#	       arrayNames = gsub(paste(sep, fileExt$green, sep=""), "", dir(pattern=fileExt$green, path=path))

+#	       if(!is.null(sampleSheet)) {

+#		       sampleSheet=NULL

+#		       cat("Could not find required info in \'sampleSheet\' - ignoring.  Check \'sampleSheet\' and/or \'arrayInfoColNames\'\n")

+#	       }

+#	       pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

+#       }

+       if(!is.null(arrayNames)) {

+               pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

+       }

+      

        if(!is.null(sampleSheet)) { # get array info from Illumina's sample sheet

 	       if(is.null(arrayNames)){

 		       ##arrayNames=NULL

@@ -41,8 +45,17 @@ readIdatFiles <- function(sampleSheet=NULL,

 		       }

 	       }

 	       pd = new("AnnotatedDataFrame", data = sampleSheet)

-	       sampleNames(pd) <- basename(arrayNames)

+	       sampleNames(pd) <- basename(arrayNames)               

+       }

+       if(is.null(arrayNames)) {

+               arrayNames = gsub(paste(sep, fileExt$green, sep=""), "", dir(pattern=fileExt$green, path=path))

+               if(!is.null(sampleSheet)) {

+                      sampleSheet=NULL

+                      cat("Could not find required info in \'sampleSheet\' - ignoring.  Check \'sampleSheet\' and/or \'arrayInfoColNames\'\n")

+               }

+               pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

        }

+       

        narrays = length(arrayNames)

        grnfiles = paste(arrayNames, fileExt$green, sep=sep)

        redfiles = paste(arrayNames, fileExt$red, sep=sep)

@@ -57,8 +70,8 @@ readIdatFiles <- function(sampleSheet=NULL,

 	       grnidats <- grnfiles

 	       redidats <- redfiles

        }

-       if(!all(file.exists(grnfiles))) stop("Missing some of the *Grn.idat files")

-       if(!all(file.exists(redfiles))) stop("Missing some of the *Red.idat files")       

+       if(!all(file.exists(grnidats))) stop("Missing some of the *Grn.idat files")

+       if(!all(file.exists(redidats))) stop("Missing some of the *Red.idat files")       

 ##       if(!all(c(redfiles,grnfiles) %in% dir(path=path))){

 ##	       stop("Missing .idat files: red\n", paste(redfiles[!(redfiles %in% dir(path=path))], sep=" "), "\n green\n",

 ##		    paste(grnfiles[!(grnfiles %in% dir(path=path))], sep=" "))

Binary files a/inst/doc/crlmmIllumina.pdf and b/inst/doc/crlmmIllumina.pdf differ

@@ -80,7 +80,7 @@ was 1.2 GB of RAM on our linux system.

 The \Robject{RG} object is an \Rclass{NChannelSet} which stores the 

 Red and Green intensities, the number of beads and standard errors for 

 each bead-type.  

-The scanning date of each array is stored in the \Robject{protocolData} slot.

+The scanning date of each array is stored in \Robject{protocolData}.

 <<explore>>=

 class(RG)

@@ -104,8 +104,8 @@ with poor signal.

 <<boxplots, fig=TRUE, width=8, height=8>>=

 par(mfrow=c(2,1), mai=c(0.4,0.4,0.4,0.1), oma=c(1,1,0,0))

-boxplot(log2(exprs(channel(RG, "R"))), xlab="Array", ylab="", main="Red channel", outline=FALSE, las=2)

-boxplot(log2(exprs(channel(RG, "G"))), xlab="Array", ylab="", main="Green channel", outline=FALSE, las=2)

+boxplot(log2(exprs(channel(RG, "R"))), xlab="Array", ylab="", names=1:40, main="Red channel", outline=FALSE, las=2)

+boxplot(log2(exprs(channel(RG, "G"))), xlab="Array", ylab="", names=1:40, main="Green channel", outline=FALSE, las=2)

 mtext(expression(log[2](intensity)), side=2, outer=TRUE)

 mtext("Array", side=1, outer=TRUE)

 @