[BioC] biomArt problems

steffen at stat.Berkeley.EDU steffen at stat.Berkeley.EDU
Mon Jan 12 21:56:19 CET 2009

Dear Arnaud,

makeGene depends on biomaRt and contains some hardcoded attrubutes that it
tries to retrieve from the Ensembl BioMart database.  As you noticed
recently the "biotype" attribute has changed in the Ensembl BioMart and
we're currently enable to retrieve that from the Ensembl BioMart.  I'm
working on a fix that eliminates the need for biotype and won't break if
some of the BioMart attributes are not found.
I should get this ready within the next couple of days and will post a fix.


> Hello Mr Durinck,
> For many months, I have used the GenomeGraphs package without any
> problems.
> But since a few days, the following code from the documentation :
> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id", biomart
> = mart)
> Gives the following error message :
> error in getBM(c("structure_gene_stable_id",
> "structure_transcript_stable_id",  :
> Number of columns in the query result doesn't equal number of attributes
> in query.  This is probably an internal error, please report.
> I think that is a problem with biomaRt.  Something have changed on the
> biomaRt server ?
> Thanks you,
> Arnaud.

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