# HG changeset patch # User fubar # Date 1374978480 14400 # Node ID 37b851eb82033c12fdb550e847e8b40ee302b3c8 # Parent 79e3d80d34f9cc5c17140f0c9005f39e52fd3135 Uploaded diff -r 79e3d80d34f9 -r 37b851eb8203 rgedgeR/rgedgeRpaired.xml --- a/rgedgeR/rgedgeRpaired.xml Sat Jul 27 22:01:16 2013 -0400 +++ b/rgedgeR/rgedgeRpaired.xml Sat Jul 27 22:28:00 2013 -0400 @@ -581,15 +581,13 @@ pdf("DESeq2_MA_plot.pdf") plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit)) dev.off() - rlogres = rlogTransformation(sresDESeq) + rlogres = rlogTransformation(resDESeq) 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)) {