plotcounts plotting vst normalized counts about rnadeseq HOT 2 CLOSED

Hi @qbicStefanC , I had a more detailed look in the plotCounts function and the plotted values are already raw counts transformed by the DESeq function:

cds <- DESeqDataSetFromMatrix( countData =count.table, colData =metadata, design = eval(parse(text=as.character(design[[1]]))))
cds <- DESeq(cds,  parallel = FALSE)
...
boxplot_counts <- plotCounts(cds, gene=i, intgroup=c("combfactor"), returnData=TRUE, normalized = T)

And according to the DESeq2 vignette, this is the recommended way of doing these boxplots: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#plot-counts
(and not with the rlog transformation or vst transformation)

What is possible, though, is to additionally display log2 of these counts, instead of the non-transformed values, with:
boxplot_counts <- plotCounts(cds, gene=i, intgroup=c("combfactor"), returnData=TRUE, normalized = T, transform=T)

Is that maybe what you meant and you would like to have?

from rnadeseq.

Hi @qbicStefanC , do you have more input here or can I close the issue?

from rnadeseq.