I would like to present the results of GOHyperG in the form of a table with GO ID, Count, Pvalue and GOTERM. The problem lies within the GOTERM ,because the output of the enviroment has changed!!! I am calling GOHyperG with a series of LOCUS IDS, ids1 ids1MF<- GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") Then I am building a matrix with the call. The matrix has the columns GO ID, Counts and pvalues. But I also want the GOTERM. The problem is that there is no function which reports the GOTERM by it self. For example mget("GO:0016407",GOTERM)) $"GO:0016407" GOID = GO:0016407 GO term = acetyltransferase activity Definition for GO term = Catalysis of the transfer of an acetyl group to an acceptor molecule. Ontology = MF But I only want the GOTERM ids1matrMF<-cbind(names(ids1MF$intCounts), as.vector(ids1MF$intCounts), as.vector(ids1MF$pvalues)) dimnames(ids1matrMF)[[2]]<-c(?GO ID?,?Counts?,?pvalues?) How can I retrieve only the GOTERM????? Thanx

Michael, Does the function getGOTerm (from GOstats) do what you want? Sean On Oct 14, 2004, at 6:01 AM, Auer Michael wrote: > I would like to present the results of GOHyperG in the form of a table > with GO ID, Count, Pvalue and GOTERM. The problem lies within the > GOTERM > ,because the output of the enviroment has changed!!! > > > > I am calling GOHyperG with a series of LOCUS IDS, ids1 > > ids1MF<- GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") > > Then I am building a matrix with the call. The matrix has the columns > GO > ID, Counts and pvalues. But I also want the GOTERM. The problem is that > there is no function which reports the GOTERM by it self. > For example mget("GO:0016407",GOTERM)) > > $"GO:0016407" > GOID = GO:0016407 > GO term = acetyltransferase activity > Definition for GO term = Catalysis of the transfer of an acetyl group > to > an acceptor molecule. > Ontology = MF > But I only want the GOTERM > > ids1matrMF<-cbind(names(ids1MF$intCounts), as.vector(ids1MF$intCounts), > as.vector(ids1MF$pvalues)) > dimnames(ids1matrMF)[[2]]<-c(?GO ID?,?Counts?,?pvalues?) > > > > How can I retrieve only the GOTERM????? > > Thanx > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Auer, I would like to do similar thing with GOTERM as you are doing at some extent but I would like to build table like : (I am using Affy chips here) GOTERM ,count of ProbeIDS associated with them , ProbeIDS itself , SYMBOLS of probe ids any idea on this ? Thanks Saurin --- Auer Michael <michael.auer@meduniwien.ac.at> wrote: > I would like to present the results of GOHyperG in > the form of a table > with GO ID, Count, Pvalue and GOTERM. The problem > lies within the GOTERM > ,because the output of the enviroment has changed!!! > > > > I am calling GOHyperG with a series of LOCUS IDS, > ids1 > > ids1MF<- > GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") > > Then I am building a matrix with the call. The > matrix has the columns GO > ID, Counts and pvalues. But I also want the GOTERM. > The problem is that > there is no function which reports the GOTERM by it > self. > For example mget("GO:0016407",GOTERM)) > > $"GO:0016407" > GOID = GO:0016407 > GO term = acetyltransferase activity > Definition for GO term = Catalysis of the transfer > of an acetyl group to > an acceptor molecule. > Ontology = MF > But I only want the GOTERM > > ids1matrMF<-cbind(names(ids1MF$intCounts), > as.vector(ids1MF$intCounts), > as.vector(ids1MF$pvalues)) > dimnames(ids1matrMF)[[2]]<-c(“GO > ID”,”Counts”,”pvalues”) > > > > How can I retrieve only the GOTERM????? > > Thanx > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >