[Bioc-sig-seq] extract gene symbol error

[Steve Lianoglou]

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 <KQu at 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 at 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