[BioC] Category

Robert Gentleman rgentlem at fhcrc.org
Tue Mar 13 20:41:01 CET 2007

Hi Lana,
   Then basically you need to
  1) download their database
  2) map from whatever gene IDs they use to EntrezGene (maybe that is 
what they are)

  3) create an incidence matrix, one row per gene set, once column per 
gene where the i,jth entry contains a 1 if gene j is in gene set i

  then you can use that matrix with virtually any annotation package and 
with most of the Category functions

  You could take a different approach and create a package that 
contained the gene sets, each one could be its own variable, and each 
gene set consists of the Entrez Gene IDs for the members. From that it 
would be reasonably easy to construct the incidence matrix described 
above, for any subset of gene sets of interest.

  best wishes

Lana Schaffer wrote:
> Seth,
> I actually want to put the GSEA curated databases(Broad Institute) into R so that they
> can be used by the Category program.  I need more disease states than what is in
> Lana
>> Hi Lana,
>> "Lana Schaffer" <schaffer at scripps.edu> writes:
>> Robert,
>> How can I add a database into your Catagory package?
>> Can you give us a bit more detail of what it is you want to do?
> + seth

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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