[BioC] GeneSetCollection using EntrezID

Javier Pérez Florido jpflorido at gmail.com
Thu Nov 19 14:20:36 CET 2009


Dear list,
I would like to carry out a Gene Set Analysis on the KEGG pathways on my 
Human Gene ST 1.0 array experiment using GSEABase. The annotation data 
included in this experiment is pd.hugene.1.0.st.v1, but it hasn't got 
functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are 
handled by hugene10sttranscriptcluster.db, so, my idea was to, first, 
using hugene10sttranscriptclusterENTREZID to get the entrezID for each 
gene in the experiment and then call GeneSetCollection using these 
entrezIDs, something like that:

GeneSetCollection(entrezIDlist, 
idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't work
Error en function (classes, fdef, mtable)  :
  unable to find an inherited method for function "GeneSetCollection", 
for signature "character", "character", "KEGGCollection"

How can I build my Gene set object?
Thanks,
Javier



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