[Bioc-devel] Change of schema of ENSEMBL biomart

Kevin Rue-Albrecht kevin.rue at ucdconnect.ie
Fri Oct 17 16:03:23 CEST 2014

Well spotted Tiphaine !

I just checked and this has affected my package (GOexpress) as well, as it
fetches the external_gene_id to annotate gene features.
This prevent the key analysis step from completing on my analysis of *Bos
taurus* gene expression as well.

Consequently, I will bug-fix the release version immediately.

For the record, I make a few different calls to biomaRt for gene ontology
annotations, and I didn't get any error message there. But as you say,
there may be other Easter eggs in the various datasets.

Thanks very much !

On 17 October 2014 14:48, Martin, Tiphaine <tiphaine.martin at kcl.ac.uk>

> Hi Everybody,
> Yesterday, I observed that ENSEMBL changed a little their schema of  the
> dataset "hsapiens_gene_ensembl".
> In my case, some of my functions were impacted by the change from
> "external_gene_id" to
> "external_gene_name".
> Maybe there are other change in this dataset or other datasets.
> Regards,
> Tiphaine
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list