[BioC] Question about GOstatsHyperG

[Sean Davis]

On Thu, Jul 10, 2008 at 11:05 AM, ss <affysnp at gmail.com> wrote:
> Dear all,
>
> Hi! I have a question about using the function 'hyperGTest' in
> GOstatsHyperG.
> What if I want to find the enriched GO terms based on a set of genes which I
> only know gene symbol, Ensembl Gene ID, and RefSeq ID. Since the array
> is customized and I don't find the corresponding 'annotation' package in
> Bioconductor.
>
> In other words, when making the:
>
> params <- new(...,geneIds, annotation,...), would it possible for me to pass
> "gene symbol"
> or "Ensembl Gene ID", or "RefSeq ID" to "geneIds" and ignore "annotation"
> etc.?

You can use the org.hs-type annotation package, which uses entrez gene
id as the key.  So, you would need to get the Entrez Gene ID for the
genes on your chip.  Given that you have RefSeq, Ensembl, and Symbol,
you can use the same annotation package to get back to Entrez Gene ID
from those other ID types.

Sean