Hi, Two things:
(1) You should update to the latest version of R (and, therefore, bioconductor). The current version of R is 2.13.1, which goes with Bioconductor 2.8 -- R 2.11.x is getting long in the tooth by now :-) The second point is inline: On Thu, Jul 21, 2011 at 8:04 PM, Kunbin Qu <k...@genomichealth.com> wrote: > Hi, I ran into error when try to build a table of gene ID and its > corresponding name. It complained about an gene ID which could not be located > from the gene symbol table. I have used update.packages to update > "GenomicFeatures" and "org.Hs.eg.db" today. Could anybody help? Thanks. > > -Kunbin > > > library(ShortRead) > library(GenomicFeatures) > library(org.Hs.eg.db) > > map <- org.Hs.egSYMBOL > hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") > Download the knownGene table ... annEx<-exonsBy(hg19KG, "gene") ...OK > Download the knownToLocusLink table ... OK > Extract the 'transcripts' data frame ... OK > Extract the 'splicings' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > annEx<-exonsBy(hg19KG, "gene") > GRList<-names(annEx) Instead of this: > geneN<-toTable(map[GRList]) To something like this: R> mget(GRList, map, ifnotfount=NA) So that you don't get an error when there is a value in GRList, that's doesn't match in `map`, like you do here: > Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : > value for "100130426" not found > Error in toTable(map[GRList]) : > error in evaluating the argument 'x' in selecting a method for > function 'toTable' Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing