Hi

I just tried it with R 2.15, I get the same error.

If I follow your suggestion:
> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")

I get:

Download the ensGene table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000513161: the cds cumulative length is not a multiple of 3
2: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000417833: the cds cumulative length is not a multiple of 3
3: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000450884: the cds cumulative length is not a multiple of 3

Hmm, what else could I try?
In any case, thanks a lot for any suggestion!!

Am 06.06.2012 um 21:59 schrieb Steve Lianoglou:

> Hi Stefanie,
> 
> On Wed, Jun 6, 2012 at 10:03 AM, Stefanie <stefanie.tauber@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

DI Stefanie Tauber

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University, Medical University, and University of Veterinary Medicine, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2
Dr. Bohr Gasse 9
A-1030 Wien, Austria
Phone: ++43 +1 / 42772-4030
Fax:     ++43 +1 / 42772-4098
email:   stefanie.tauber@univie.ac.at
www.cibiv.at


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