[BioC] DESeq gene names under id

Simon Anders anders at embl.de
Tue Nov 29 23:12:52 CET 2011

Hi Mary Ann

> In the manual "Analysing RNA-Seq data with the\DESeq" package" I
> followed the directions exactly. However, I get something slightly
> different.
> http://bioconductor.org/packages/2.9/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
> When I use the command (page 7)
> res <- nbinomTest( cds, "N", "T" )
> I get numbers under ids because on page 4 we removed the gene names.
> countsTable <- countsTable[ , -1 ]
> How can i get my res to match what is in the manual with gene names
> under id?

WIth the line
    countsTable <- countsTable[ , -1 ]
we removed the gene IDs, but with the preceding line,
    rownames(countsTable) <- countsTable[,1]
we copied them into the data frame's 'rownames' attribute, where DESeq 
find them and then uses them later. Maybe you have omitted this step.


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