[BioC] makeTranscriptDbFromBiomart error

[Steve Lianoglou]

Hi Stefanie,

On Wed, Jun 6, 2012 at 10:03 AM, Stefanie <stefanie.tauber at univie.ac.at> wrote:
> Hi,
>
> here is my code:
> library(GenomicFeatures)
> humanDB = makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
> "hsapiens_gene_ensembl")
>
> This is the error I get thrown:
> Download and preprocess the 'transcripts' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Download and preprocess the 'splicings' data frame ... Fehler in
> .extractCdsRangesFromBiomartTable(bm_table) :
>  BioMart data anomaly: some 5' UTR have a start > end
>
> Seems to be a problem of biomart not of R?
> Anybody any idea?

I don't think this is the problem, but I'd first start by updating R
to 2.15.x and reinstall your bioconductor packages (via `biocLite`) so
that your playing w/ the latest and greatest.

Second, you might try building the DB you need via UCSC using their
ensGene table ... I guess it should be pretty much what you need, no?
For example:

R> library(GenomicFeatures)
R> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")

HTH,
-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