Mercurial > repos > fubar > differential_count_models

changeset 23:37b851eb8203 draft

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Uploaded
author fubar
date Sat, 27 Jul 2013 22:28:00 -0400
parents 79e3d80d34f9
children 48d71bd383a1
files rgedgeR/rgedgeRpaired.xml
diffstat 1 files changed, 1 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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)) {