Browse code

changed outdir for copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@49111 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 15:45:40
Showing2 changed files

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@@ -72,4 +72,3 @@ export(crlmm,
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 ##export(initializeParamObject, biasAdjNP2)
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-exportMethods(totalCopyNumber)
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\ No newline at end of file
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@@ -43,7 +43,6 @@ options(continue=" ", width=70)
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 CRLMM supports the following platforms:
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 <<cdfname>>=
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-library(oligoClasses)
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 library(crlmm)
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 crlmm:::validCdfNames()
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 cdfName <- "genomewidesnp6"
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@@ -60,8 +59,13 @@ array as a surrogate for batch. Adjusting by date or chemistry plate
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 can be helpful for limiting the influence of batch effects.
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 <<celfiles>>=
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-celFiles <- list.celfiles("/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m", full.names=TRUE, pattern=".CEL")
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-outdir <- "/thumper/ctsa/snpmicroarray/rs/data/hapmap/crlmmVignette/release/affy"
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+if(getRversion() < "2.12.0"){
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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, "/affy_vignette", sep="")
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+datadir <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"
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+celFiles <- list.celfiles(datadir, full.names=TRUE, pattern=".CEL")
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+##outdir <- "/thumper/ctsa/snpmicroarray/rs/data/hapmap/crlmmVignette/release/affy"
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 dir.create(outdir, showWarnings=FALSE)
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 ## CEPH and Yoruban
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 batch <- substr(basename(celFiles), 13, 13)