R novice here, trying to use DESeq (which is working well, by the way) 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/DES eq.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? Thanks, Mary Ann Allen

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/D ESeq.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. Simon