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comparison rgedgeRpaired_nocamera.xml @ 128:999d4b5939bb draft

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author fubar
date Thu, 27 Nov 2014 19:18:10 -0500
parents 731315bd6e48
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127:23afddb3d1e5 128:999d4b5939bb
536 Name=as.character(rownames(myDGEList)), 536 Name=as.character(rownames(myDGEList)),
537 DE\$table, 537 DE\$table,
538 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), 538 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
539 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums 539 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
540 ) 540 )
541 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
542 stt = tt[order(DE\$table\$PValue),]
541 print.noquote("@@ edgeR Top tags\n") 543 print.noquote("@@ edgeR Top tags\n")
542 tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely 544 print.noquote(stt[1:50,])
543 print.noquote(tt[1:50,])
544 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,]) 545 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
545 nsig = length(deTags) 546 nsig = length(deTags)
546 print.noquote(paste('@@',nsig,'tags significant at adj p=',fdrthresh)) 547 print.noquote(paste('@@',nsig,'tags significant at adj p=',fdrthresh))
547 deColours = ifelse(deTags,'red','black') 548 deColours = ifelse(deTags,'red','black')
548 pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_")) 549 pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_"))