On Tue, Nov 8, 2011 at 3:19 AM, Tim Rayner <tfrayner@gmail.com> wrote:

> Hi,
>
> I'm trying to make a TranscriptDb from the Ensembl human Biomart, but
> I've run into a problem. As shown below, the equivalent operation for
> the mouse Biomart works fine:
>
> > # Mouse TranscriptDb created without a hitch:
> > txdb.Mm <- makeTranscriptDbFromBiomart(biomart='ensembl',
> dataset='mmusculus_gene_ensembl')
> Download and preprocess the 'transcripts' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Download and preprocess the 'splicings' data frame ... OK
> Download and preprocess the 'genes' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> Make the TranscriptDb object ... OK
>
> > # Here's the problem:
> > txdb.Hs <- makeTranscriptDbFromBiomart(biomart='ensembl',
> dataset='hsapiens_gene_ensembl')
> Download and preprocess the 'transcripts' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
> Download and preprocess the 'splicings' data frame ... Error in
> scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>  line 800380 did not have 11 elements
>
> > sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicFeatures_1.6.1 AnnotationDbi_1.16.0  Biobase_2.14.0
> [4] GenomicRanges_1.6.1   IRanges_1.12.1
>
> loaded via a namespace (and not attached):
>  [1] BSgenome_1.22.0    Biostrings_2.22.0  DBI_0.2-5          RCurl_1.6-10
>  [5] RSQLite_0.10.0     XML_3.4-3          biomaRt_2.10.0
> rtracklayer_1.14.1
>  [9] tools_2.14.0       zlibbioc_1.0.0
>
> I don't know if this is an issue with the Biomart instance or the
> GenomicFeatures package. I was wondering if anyone had any suggestions
> as to how I might work around this?
>
> On a related note, would it be possible to add the ability to point
> makeTranscriptDbFromBiomart() at alternate Biomart hosts (as one
> would, for example, by calling
> biomaRt::useMart(host='www.ensembl.org', ...))?


We've submitted a patch that does just this, as well as supporting an
attribute prefix string for selecting alternative gene models.


> It would probably be
> good to be able to pass through the 'archive' argument to useMart as
> well.
>
> Many thanks,
>
> Tim Rayner
>
> --
> Bioinformatician
> Smith Lab, CIMR
> University of Cambridge
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

