[BioC] KEGG package

[Weiwei Shi]

Hi, Yihuan:

Check the following link:
http://www.broad.mit.edu/gsea/wiki/index.php/Msigdb_may_2006_release_notes

and you will find KEGG has been built into MsigDB of GSEA.

So, if your purpose is GSEA analysis, the only thing you need to do is
map your ACC number to Entrezgene id. John's suggestion is also
helpful if you try to use KEGG package in BioC.

BTW, I recommend you use desktop version of GSEA since it takes me a
lot of trouble to change the codes of R's version ( I believe there is
a bug and report it to GSEA group already and I believe they are
working on that now).

HTH,

Weiwei

On 8/13/07, John Zhang <jzhang at jimmy.harvard.edu> wrote:
>
> >
> >I would like to use GSEA to analyze customed microarrays. I need to map genes
> from ACC number to KEGG pathways. How can I do it using KEGG package? I could
> not find any documents for KEGG package. Is there any example?
>
>
> Try the following in R to see if there is anything helpfull:
>
> >KEGG()
> >?KEGG
> >?KEGGEXTID2PATHID (or any of the environment in KEGG)
>
>
>
>
>
>
> >
> >Best,
> >
> >Yihuan
> >
> >_______________________________________________
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> >Bioconductor at stat.math.ethz.ch
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>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
> _______________________________________________
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>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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