Mercurial > repos > fubar > differential_count_models
changeset 22:79e3d80d34f9 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 27 Jul 2013 22:01:16 -0400 |
| parents | 1fe9db11189b |
| children | 37b851eb8203 |
| files | rgedgeR/rgedgeRpaired.xml |
| diffstat | 1 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/rgedgeR/rgedgeRpaired.xml Sat Jul 27 20:59:23 2013 -0400 +++ b/rgedgeR/rgedgeRpaired.xml Sat Jul 27 22:01:16 2013 -0400 @@ -534,8 +534,8 @@ #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg))) efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors normData = (1e+06*dg\$counts/efflib) - outpdfname="edgeR_heatmap.pdf" - hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=myTitle) + outpdfname="edgeR_top_100_heatmap.pdf" + hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle)) outSmear = "edgeR_smearplot.pdf" outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='') smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain) @@ -581,13 +581,15 @@ pdf("DESeq2_MA_plot.pdf") plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit)) dev.off() - rlogres = rlogTransformation(resDESeq) + rlogres = rlogTransformation(sresDESeq) sampledists = dist( t( assay(rlogres) ) ) sdmat = as.matrix(sampledists) pdf("DESeq2_sample_distance_plot.pdf") heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"), col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) dev.off() + outpdfname="DESeq2_top100_heatmap.pdf" + hmap2(rlogres,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 Heatmap',myTitle)) sink() result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) ) if ("try-error" %in% class(result)) {