in http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, it used three types of data to plot heatmap
ntd <- normTransform(dds) vsd <- vst(dds, blind=FALSE) rld <- rlog(dds, blind=FALSE)
which data is right? and there is also another function
normalized_counts <- counts(dds, normalized=TRUE)
how to select?
I also found a problem, I used deseq2 to find significant genes, and select the most differenet genes, and used vsd data to plot heatmap, but the plot obsviously not show high contrast color in two groups
can you help me, thanks a lot. by the way, deseq2 can automatically discard low exression genes when does diff analysis, is it right?