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"Piero Cantone" <piero.cantone at="" gmail.com=""> writes: > Dear mailinglist, > > I am new to bioconductor, and I have a simple task to performs, so I would > like to ask for yours assistance. I have to analyze an old gene expression > experiment, performed on 5 microarray chip: mu11kA mu11kB, mgu74B, mgu74C2, > and an old GEM platforms for with I have accession number as univocal IDs. I > need to check for some GO terms previously defined by my previously; in > particular I have to retrive all the member.s of the terms in mus musculus, > and then check for intersection with differentially regulated genes. > > So in contrast to the typical procedure, I am not looking for enriched > categories, but for some specific terms, regardless of their enrichments (at > least in the beginning). I looked in manual and Workshop, but I can't make > it up. > I tried > >> tmp=as.list(GOALLENTREZ) >> match(tmp, my_entrez, nomatch=0) > > but I didn't find matches. Actually i think this is because GOALLENTREZ > provides entrez from different species. furthermore HyperG function in > GOstats requires the definition of a chip, but in my case it is a little bit > more complicated. > > > which strategy would you suggest? Perhaps the mouseLLMappings package would be a better place to start? my_matches = eapply(mouseLLMappingsGO2LL, function(egids) intersect(my_entrez, egids)) And the above eapply approach should also work with GOALLENTREZ, but since this contains data for multiple organisms it will be slower. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org