@@ -151,3 +151,7 @@ is decoded and scanned

 2009-04-27 R Scharpf - committed version 1.3.1

 * Fixed bug in nonpolymorphic() function

+

+2009-05-07 Matt Ritchie - committed version 1.3.2

+

+* Updated usage of sampleNames() on NChannelSet objects in Illumina functions to maintain consistency with Biobase

@@ -1,7 +1,7 @@

 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: 1.3.1

+Version: 1.3.2

 Date: 2008-12-30

 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>

@@ -457,7 +457,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

 #  brgrg = bids[rrgg]

   X = Y = Xnb = Ynb = Xse = Yse = zero = matrix(0, nsnps, narrays)

   rownames(X) = rownames(Y) = rownames(Xnb) = rownames(Ynb) = rownames(Xse) = rownames(Yse) = ids

-  colnames(X) = colnames(Y) = colnames(Xnb) = colnames(Ynb) = colnames(Xse) = colnames(Yse) = sampleNames(RG)$G

+  colnames(X) = colnames(Y) = colnames(Xnb) = colnames(Ynb) = colnames(Xse) = colnames(Yse) = sampleNames(RG) #$G

   # First sort out Infinium II SNPs, X -> R (allele A)  and Y -> G (allele B) from the same probe

   X[!is.na(aord),] = exprs(channel(RG, "R"))[aord[!is.na(aord)],] # mostly red

@@ -529,7 +529,7 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

     targetdist = getVarInEnv("reference")

   Xqws = Yqws = matrix(0, nrow(XY), ncol(XY))

-  colnames(Xqws) = colnames(Yqws) = sampleNames(XY)$X

+  colnames(Xqws) = colnames(Yqws) = sampleNames(XY) #$X

   rownames(Xqws) = rownames(Yqws) = featureNames(XY)

   if(verbose){

@@ -574,7 +574,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5, fitMixture=TRUE, eps=

     XY = stripNormalize(XY, useTarget=useTarget, verbose=verbose)

 ## MR: the code below is mostly straight from snprma.R

-  if (missing(sns)) sns <- sampleNames(XY)$X

+  if (missing(sns)) sns <- sampleNames(XY) #$X

   if(missing(cdfName))

     cdfName <- annotation(XY)

 ##  stuffDir <- changeToCrlmmAnnotationName(cdfName)

@@ -707,7 +707,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

       else

         stop("Both RG and XY specified - please use one or the other")

     }

-    if (missing(sns)) sns <- sampleNames(XY)$X

+    if (missing(sns)) sns <- sampleNames(XY) #$X

     res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                         seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget,