[BioC] biomaRt zebrafish

[sdurinck@ebi.ac.uk]

Dear Georg,

In the last release of Ensembl the zebrafish array hasn't been included,
along with 3 other arrays that were present in the previous release.  I am
contacting the Ensembl people to see why this has happened (it looks like
they just forgot to include it).  For now a possible solution
could be to work with a local installation of ensembl_mart_31 (see the
archives on www.ensembl.org).  I expect zebrafish to be included again in
the next Ensembl release.

Note that the latest biomaRt version should be downloaded from the
developmental packages, the current version is 1.1.8

best regards,
Steffen


Dear Bioconductors,

I have a question concerning biomaRt.

I am running biomaRt 1.0.4 (which I think should be the newest version)
on R 2.1.0

In the vignette, "Description of the biomaRt package" in chapter 3.11 it is
shown how the command:

mart<-martConnect()
getAffyArrays(mart = mart)

retrives a list of Affymetrix identifiers which are present in ensembl, and
among those there is also the zebrafish array.

However, when I reproduce this, I get a list of Affymtrix arrays, but the
zebrafish array is missing.

My question is now: what happened to the zebrafish array in ensembl? Has it
been removed? Or is this a problem with my version of biomaRt?

Thanks for your help!

Georg

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