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 | ... | ... |
@@ -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) |