diff rgedgeR/rgedgeRpaired.xml @ 22:79e3d80d34f9 draft

Uploaded

--- 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)) {