[BioC] How to filter a list of genes by their ontology

[James W. MacDonald]

Hi Laurent,

On 9/17/2012 11:15 AM, Laurent Pays [guest] wrote:
> Hi,
> After analysing my arrays for differentially expressed genes, I get a list of genes Id. To reduce even more the number of genes in this list, I would like to retain only genes related to the immune system. I've looked for packages dealing with "ontology" but I couldn't find any doing this simple task...
>
> Any idea on what package/function I could use?
>
> Thanks in advance for your help.
>
> L.P
>
>   -- output of sessionInfo():
>
> R version 2.7.0 (2008-04-22)
> powerpc-apple-darwin8.10.1

Seriously, you need to upgrade. A four year old version of R is 
ridiculously outdated.

Best,

Jim


>
> locale:
> fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099