Mercurial > repos > fubar > differential_count_models

diff rgedgeRpaired_nocamera.xml @ 128:999d4b5939bb draft

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author fubar
date Thu, 27 Nov 2014 19:18:10 -0500
parents 731315bd6e48
children
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--- a/rgedgeRpaired_nocamera.xml	Thu Nov 27 18:39:15 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Thu Nov 27 19:18:10 2014 -0500
@@ -538,9 +538,10 @@
     adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
     Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
   )
+  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
+  stt = tt[order(DE\$table\$PValue),]
   print.noquote("@@ edgeR Top tags\n")
-  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
-  print.noquote(tt[1:50,])
+  print.noquote(stt[1:50,])
   deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
   nsig = length(deTags)
   print.noquote(paste('@@',nsig,'tags significant at adj p=',fdrthresh))