[BioC] GOstats testing using EntrezGene IDs not in chip-specific annotation package?

[Marc Carlson]

Hi Jenny,

As Heidi says, this really should work with org packages.  Please let me
know if you find a case where it doesn't.  And, in that case, please
send me a specific example so that I can fix it.


  Marc



Heidi Dvinge wrote:
> <snip>
>
>   
>> Mainly my
>> question is why does the GOstats hyperGTest() require a chip-specific
>> annotation package when you have to input EntrezGene IDs (the
>> mapping  key for the org.Xx.eg.db packages), not probe set
>> IDs?  Could hyperGTest()  be (easily) modified to directly accept the
>> org.Xx.eg.db packages?
>>
>>     
> It already does :) At least when I use hyperGTest() from the Category
> package for GO/KEGG/Chrlocation, it works fine with org.Mm.eg.db. I
> actually don't know whether there are any differences between hyperGTest()
> from GOstats and the one from Category.
>
> Cheers
> \Heidi
>
>   
>> Thanks,
>> Jenny
>>
>> Jenny Drnevich, Ph.D.
>>
>> Functional Genomics Bioinformatics Specialist
>> W.M. Keck Center for Comparative and Functional Genomics
>> Roy J. Carver Biotechnology Center
>> University of Illinois, Urbana-Champaign
>>
>> 330 ERML
>> 1201 W. Gregory Dr.
>> Urbana, IL 61801
>> USA
>>
>> ph: 217-244-7355
>> fax: 217-265-5066
>> e-mail: drnevich at illinois.edu
>>
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>>     
>
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