Mercurial > repos > fubar > differential_count_models

comparison rgedgeR/rgedgeRpaired.xml @ 23:37b851eb8203 draft

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author fubar
date Sat, 27 Jul 2013 22:28:00 -0400
parents 79e3d80d34f9
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comparison
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22:79e3d80d34f9 23:37b851eb8203
579 ybig = abs(max(rDESeq\$log2FoldChange)) 579 ybig = abs(max(rDESeq\$log2FoldChange))
580 ylimit = min(4,ysmall,ybig) 580 ylimit = min(4,ysmall,ybig)
581 pdf("DESeq2_MA_plot.pdf") 581 pdf("DESeq2_MA_plot.pdf")
582 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit)) 582 plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
583 dev.off() 583 dev.off()
584 rlogres = rlogTransformation(sresDESeq) 584 rlogres = rlogTransformation(resDESeq)
585 sampledists = dist( t( assay(rlogres) ) ) 585 sampledists = dist( t( assay(rlogres) ) )
586 sdmat = as.matrix(sampledists) 586 sdmat = as.matrix(sampledists)
587 pdf("DESeq2_sample_distance_plot.pdf") 587 pdf("DESeq2_sample_distance_plot.pdf")
588 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"), 588 heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
589 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) 589 col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
590 dev.off() 590 dev.off()
591 outpdfname="DESeq2_top100_heatmap.pdf"
592 hmap2(rlogres,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 Heatmap',myTitle))
593 sink() 591 sink()
594 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) ) 592 result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
595 if ("try-error" %in% class(result)) { 593 if ("try-error" %in% class(result)) {
596 print.noquote('DESeq2 plotPCA failed.') 594 print.noquote('DESeq2 plotPCA failed.')
597 } else { 595 } else {