Changes between Version 1 and Version 2 of SOPs/rna-seq-diff-expressions/DESeq

Timestamp:

06/28/13 14:26:57 (11 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions/DESeq

@@ -25 +25 @@
  results = nbinomTest(cds, "T", "C")
  write.table(results, file="DESeq_output.txt", sep="\t", quote=F)
+
+ # Data quality assessment by sample clustering and visualisation (optional)
+ library(gplots)
+ library("RColorBrewer")
+ #re-estimate dispersion with method "blind" to ensure analysis is unbiased.
+ cdsFullBlind=estimateDispersions(cds, method="blind")
+ #vst needed for PCA and heatmap
+ vsd=varianceStabilizingTransformation(cdsFullBlind)
+
+ #do heatmap 
+ dists=dist(t(exprs(vsd)))
+ mat=as.matrix(dists)
+ rownames(mat) = colnames(mat) = with(pData(cds), paste(groups, sep=" : "))
+ hmcol = colorRampPalette(brewer.pal(9, "GnBu"))(100)
+ heatmap.2(mat, trace="none", col = rev(hmcol), margin=c(13, 13))
+
+ #do PCA
+ print(plotPCA(vsd, intgroup=c("condition")))
+
 }}}