I would like to use the hyperGTest in package "GOstats" on some
proteomics data that I have. It is LCMS data and I have a list of all
Entrez Gene identifiers of all identified proteins (the universe) and of
the significant proteins. Because of the nature of proteomics data, some
of the identified proteins are mouse, some human, and some rat. This
makes it impossible to pass the annotation package parameter to
hyperGTest.

 

I imagine this is because hyperGTest relies on the Bioc metadata
packages to map EntrezGene to GO categories. It seems to me that there
should be a work around to this problem using biomaRt or some direct
calls to the GO website. 

 

Suggestions?

 

Mark

 

Mark W. Kimpel MD 

 

 

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Department of Psychiatry

Indiana University School of Medicine

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