DeSeq and EdgeR Annotation

[Palgrave]

Hi all,

I have a gene list with refseq names as input for DeSeq and EdgeR (using both), I want to add official gene names for the output as well. I tried the following in EdgeR but it did not work:

library(org.Hs.eg.db)
idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
y <- y[idfound,]
dim(y)

Any good ways to do it?

[Gordon Smyth]

The oral carcinoma case study in the edgeR User's Guide gives a fully worked example in which this is done.

Make sure you are using a recent version of edgeR.

For more detailed help about how to use Bioconductor annotation packages, it would be best to post a question to the Bioconductor mailing list.

Gordon