[BioC] GOstats testing using EntrezGene IDs not in chip-specific annotation package?
heidi at ebi.ac.uk
Fri Jan 29 00:09:08 CET 2010
> 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.
> 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
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
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