[BioC] Access to archived versions of Ensembl with biomaRt

[mjonczyk]

Hi Adrian,

First of all, I've also seen that something changes. My best advice
is that you could submit listMarts(), choose the one closest to
previously used and see if listDatasets() will give you expected
organisms.

I've used plant database, some time ago it was "ENSEMBL_MART_PLANT",
then I have to use "plants_mart_10", recently it changed back to
"ENSEMBL_MART_PLANT". I've to mention that both databases contained
the same species, but the most recent contains also three new.
It haven't seem that versions of genomes changed.

HTH,
Maciej Jończyk

> I used to access Ensembl 54 database with the biomaRt package. The 
> command
> below was taken from one of the biomaRt tutorials on the bioconductor
> website. This commands used to work properly and I was able to query 
> the
> database but something has recently changed I believe, as this 
> command
> doesn't work anymore. I have updated my packages and R...  Any clues 
> how
> can I still query this version? What I want to do is work in hg18
> coordinates, for this reason I am querying the archived db.
>
>
> ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="
may2009.archive.ensembl.org/biomart/martservice/",
dataset='hsapiens_gene_ensembl')
>
> Error in bmAttrFilt("attributes", mart, verbose = verbose) :
   biomaRt error: looks like we're connecting to incompatible version of
BioMart suite.


-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



-- 
This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com