@@ -109,9 +109,6 @@ assign these identifiers to the variable \Robject{batch}.

 celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")

 celFiles <- celFiles[substr(basename(celFiles), 13, 13) %in% c("C", "Y")]

 batch <- as.factor(substr(basename(celFiles), 13, 13))

-sample.index <- c(sample(which(batch == "C"), 15), sample(which(batch == "Y"), 11))

-celFiles <- celFiles[sample.index]

-batch <- batch[sample.index]

 @

 The preprocessing steps for copy number estimation includes quantile

@@ -193,10 +190,7 @@ The \Rfunction{crlmmCopynumber} performs the following steps:

 <<LDS_copynumber>>=

 GT.CONF.THR <- 0.8

-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,

-		     MIN.SAMPLES=12)

-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,

-		     MIN.SAMPLES=11)

+cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR)

 @

 In an effort to reduce I/O, the \Rpackage{crlmmCopynumber} function no