Hi I want to convert the drosgenome1GO environment to a matrix with columns: Affy-probe_id, GOID, GOEvidence, GOOntology I have figured out that if I do: lis <- as.list(drosgenome1GO) lis2 <- lis[!is.na(lis)] m <- matrix(unlist(lis2), ncol=3, byrow=TRUE) I get something approaching what I want (ie a matrix with columns GO ID, GO Evidence and GO Ontology), but I also want the actual affy probe ids in there as a column (I eventually want to do a table join from the output of topTable() to this table) Thanks Mick

Hi Michael, fun = function(i) { res = matrix(unlist(lis[[i]]), ncol=3, byrow=TRUE) cbind(rep(names(lis)[i], nrow(res)), res) } z = do.call("rbind", lapply(seq(along=lis), fun)) will do (see below), I wonder if anybody can give a simpler solution! Best wishes Wolfgang > z [,1] [,2] [,3] [,4] [1,] "155157_at" "GO:0006281" "NAS" "BP" [2,] "155157_at" "GO:0016538" "ISS" "MF" [3,] "155157_at" "GO:0016538" "NAS" "MF" [4,] "155122_at" NA NA NA [5,] "155036_at" NA NA NA [6,] "154985_at" NA NA NA [7,] "154948_at" "GO:0003743" "ISS" "MF" [8,] "154948_at" "GO:0005085" "IDA" "MF" [9,] "154948_at" "GO:0005085" "ISS" "MF" michael watson (IAH-C) wrote: > Hi > > I want to convert the drosgenome1GO environment to a matrix with > columns: > > Affy-probe_id, GOID, GOEvidence, GOOntology > > I have figured out that if I do: > > lis <- as.list(drosgenome1GO) > lis2 <- lis[!is.na(lis)] > m <- matrix(unlist(lis2), ncol=3, byrow=TRUE) > > I get something approaching what I want (ie a matrix with columns GO ID, > GO Evidence and GO Ontology), but I also want the actual affy probe ids > in there as a column (I eventually want to do a table join from the > output of topTable() to this table) > > Thanks > Mick ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber