[Bioc-devel] Change of schema of ENSEMBL biomart

[Kevin Rue-Albrecht]

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 !
Kevin







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

> 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
>
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>
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-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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