[BioC] Help using ENSMUSG ids in GOstats

[Robert Gentleman]

John Reid wrote:
> Hi,
> 
> I have some sets of genes I wish to test for enrichment against a 
> background set of genes. These genes are identified by Ensembl 
> identifiers. I have found it quite straightforward to use the topGO 
> package to do this.
> 
> I would also like to use the GOstats package and test for enrichment 
> against KEGG pathways. It looks as if I need to create an annotation 
> package to do this. Is this straightforward? I didn't find out how to do 
> it from the documentation. My guess is that someone has been in this 

  Hi John,
    You don't give us much to work from.

I am guessing you have not looked at either AnnotationDbi or AnnBuilder 
as packages that you can use to build an annotation package.

    I am also guessing you have not searched the email list archives for 
any of the several previous discussions (that is a good place to start).

   You don't tell us what organism, but I suspect that you could simply 
use one of the organism based annotation packages (without needing to 
build anything).  There are several previous threads on how to do that.

   Best wishes
     Robert

> situation before. I should say the genes come from a computational 
> analysis and not from a microarray.
> 
> Any help appreciated,
> John.
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
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206-667-7700
rgentlem at fhcrc.org