[BioC] GO.db redundance

[mcarlson at fhcrc.org]

Hi Giacomo,

The problem isn't with the databases or the annotation packages, but
with how you are using toTable().  I would not use toTable() like that  
since this is not what it was designed to do.  Instead, I would  
recommend an approach more like this:

library("mgu74av2.db")
library("GO.db")

##Get the IDs you wanted
all_probes_mgu <- ls(mgu74av2ENTREZID)
##Get the GO IDs for these IDs
GOIDs = mget(all_probes_mgu, mgu74av2GO, ifnotfound=NA)

##You also wanted to remove things that were not part of the
##"CC" ontology.  There is a good way to do this in ever so convenient
##annotate package...
##So for example, we can make use of the getOntology method like this:
library("annotate")
clnList = lapply(GOIDs, getOntology, "CC")

##Finally if we want to get more details for each of these GOIDs, we
##can use the GOTERM mapping in the usual way:

##So for the probe you used in your example:
clnList[1]
##You can look up the details from the GOTERM table like this:
mget(clnList[[1]],GOTERM,ifnotfound=NA)


You weren't super clear about what exactly you were trying to do, so I  
hope that this answers your questions.  If not, please let us know.


    Marc





Quoting 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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:     
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>