Hi!

I try to follow this tutorial:

http://www.bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf

Im struggling with this part:

"Each row of the DEXSeqDataSet contains in each column the count data from a given exon (’this’) as well as the count data from the sum of the other exons belonging to the same gene (’others’). "

I have done all the previous steps according to the same tutorial (only I used NCBI instead of Ensembl), but how do I calculate "others" exons?

Thank you. 

You don't do this explicitly. As long as your data is properly preprocessed and the rowData of your DEXSeqDatSet object looks like you see here at the top of page 10 of the DEXSeq vignette, it should just work.

It's been a while since I've used DEXSeq myself, but I believe the important columns for enabling the "this" vs "others" calculations are the featureID and groupID columns you see there.

Just to confirm what Steve already said, the "others" column will be calculated when creating the DEXSeqDataSet object. So there is no need to do it by yourself.