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

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21:1fe9db11189b

  dev.off()
  dg = DGEList[order(DE\$table\$PValue),]
  #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)
  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)
  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
  norm.factor = DGEList\$samples\$norm.factors

    ybig = abs(max(rDESeq\$log2FoldChange))
    ylimit = min(4,ysmall,ybig)
    pdf("DESeq2_MA_plot.pdf")
    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
    dev.off()
    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()
    sink()
    result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
    if ("try-error" %in% class(result)) {
         print.noquote('DESeq2 plotPCA failed.')
         } else {

22:79e3d80d34f9

  dev.off()
  dg = DGEList[order(DE\$table\$PValue),]
  #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_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)
  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
  norm.factor = DGEList\$samples\$norm.factors

    ybig = abs(max(rDESeq\$log2FoldChange))
    ylimit = min(4,ysmall,ybig)
    pdf("DESeq2_MA_plot.pdf")
    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
    dev.off()
    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)) {
         print.noquote('DESeq2 plotPCA failed.')
         } else {