Entering edit mode
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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