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Remove code used for testing MIN.SAMPLES

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52846 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:59:02
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@@ -109,9 +109,6 @@ assign these identifiers to the variable \Robject{batch}.
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 celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")
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 celFiles <- celFiles[substr(basename(celFiles), 13, 13) %in% c("C", "Y")]
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 batch <- as.factor(substr(basename(celFiles), 13, 13))
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-sample.index <- c(sample(which(batch == "C"), 15), sample(which(batch == "Y"), 11))
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-celFiles <- celFiles[sample.index]
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-batch <- batch[sample.index]
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 @
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 The preprocessing steps for copy number estimation includes quantile
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@@ -193,10 +190,7 @@ The \Rfunction{crlmmCopynumber} performs the following steps:
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 <<LDS_copynumber>>=
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 GT.CONF.THR <- 0.8
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-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,
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-		     MIN.SAMPLES=12)
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-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,
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-		     MIN.SAMPLES=11)
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+cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR)
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 @
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 In an effort to reduce I/O, the \Rpackage{crlmmCopynumber} function no