[BioC] GSEABase GOCollection wrong ontology

Hans-Ulrich Klein h.klein at uni-muenster.de
Fri Feb 27 21:50:51 CET 2009


Dear All,

I want to generate sets of probes from the affy hgu133plus2 chip from 
the GO "Molecular Function". I used the GSEABase package:

 > library("GSEABase")
 > sets = 
GeneSetCollection(idType=AnnotationIdentifier("hgu133plus2.db"), 
setType=GOCollection(ontology="MF"))
 > sets[[1]]
setName: GO:0000002
geneIds: 1557631_at, 202825_at, ..., 203466_at (total: 5)
geneIdType: Annotation (hgu133plus2.db)
collectionType: GO
  ids:  (0 total)
  evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND
  ontology: MF
details: use 'details(object)'

The Gene Ontology web site says that the id "GO:0000002" belongs to 
"biological process". Something went wrong...

Regards,
Hans-Ulrich



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