[BioC] GO.db redundance

[giacomo.tuana at unimib.it]

   Hi,
   I found a redundance in GO annotation database trying to build a global
   table of annotation with probeset_ID, DB crossreferences (entrez_ID, gene
   name....) and GO annotation. For a single probe there are more GO terms very
   similar (use of synonymous) or equal (different punctuation) in GO term
   definitions; I think this could be a problem for functional annotation. Can
   someone suggest me how to deal with this situation? Or different way to
   build a global table of annotation?
   Here the code I used for CC category, example with "100001_at" probeset ID:
   library("mgu74av2.db")
   library("GO.db")
   go_mgu<-toTable(mgu74av2GO)
   go_term_description<-toTable(GOTERM)
   all_probes_mgu <- ls(mgu74av2ENTREZID)
   go_mgu_descr<-merge(go_mgu[,1:3],go_term_description,by.x=2,by.y=1)
   go_mgu_cc<-go_mgu_descr[which((go_mgu_descr[,6])=="CC"),]
   go_mgu_cc[which((go_mgu_cc[,2]=="100001_at")),]
   Thanks
   Giacomo
   --
   Dr. Giacomo Tuana Franguel
   Genopolis Consortium
   University of Milano-Bicocca
   Dept. of Biotechnology and Bioscience/ U4
   Piazza della Scienza 4 20126 Milano, Italy