[BioC] ENTREZ identifiers for PGSEA

James MacDonald jmacdon at med.umich.edu
Wed Jul 9 12:49:37 CEST 2008

You could use the findLargest() function in Biobase to select identifers 
that have the largest differences between your samples.



Sebastien Gerega wrote:
> Hi,
> I would like to use a lumi expression set with the PGSEA package and GO 
> to generate genesets. I understand that the identifiers used in the data 
> matrix need to be the same as those used in the genesets. Therefore, 
> since I am using the GO database I need to use the ENTREZ identifiers 
> for my matrix. How can I go about doing this? Obviously I cannot have 
> multiple rows with the same name so I will have to remove duplicates and 
> should probably do so based on variance or something. Is there an 
> elegant way to do what I need?
> thanks,
> Sebastien
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James W. MacDonald, MS
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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