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steffen@stat.Berkeley.EDU
▴
600
@steffenstatberkeleyedu-2907
Last seen 10.3 years ago
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.
Cheers,
Steffen
> 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.
>