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commented another cat statement inside readIdatFiles

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52842 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:47
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@@ -54,6 +54,8 @@ separately) that are listed below.
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 pkgs <- annotationPackages()
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 pkgs <- pkgs[grep("Crlmm", pkgs)]
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 pkgs
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+library(snow)
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+setCluster(4, "SOCK")
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 @
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 Note that 'pd.genomewidesnp6' and 'genomewidesnp6Crlmm' are both
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@@ -71,7 +73,8 @@ pathToCels <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"
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 if(getRversion() < "2.13.0"){
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 	rpath <- getRversion()
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 } else rpath <- "trunk"
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-outdir <- paste("/thumper/ctsa/snpmicroarray/rs/ProcessedData/crlmm/", rpath, "/copynumber_vignette", sep="")
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+##outdir <- paste("/thumper/ctsa/snpmicroarray/rs/ProcessedData/crlmm/", rpath, "/copynumber_vignette", sep="")
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+outdir <- "~/tmp"
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 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)
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 @
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@@ -105,7 +108,7 @@ we extract the population identifier from the CEL file names and
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 assign these identifiers to the variable \Robject{batch}.
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 <<celfiles>>=
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-celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")
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+celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")[1:10]
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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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 @