Hi Gareth,
I suspect you're connecting directly through biomart central, and I
don't think they've repacked/restarted their servers yet, as Arek
mentioned a slight lag due to a reorganisation of their services. I
imagine you can point your biomaRt adaptor directly at the EBI mart
servers/dbs (e.g. bacteria.ensembl.org/biomart/martview or
[email protected]:4157), though I confess this is something I
don't know much about. Maybe someone else can suggest how to modify
things to use EBI directly?
Best,
Dan.
On 03/08/2012 06:46 PM, Gareth Morgan wrote:
Thanks Dan. I guessed that it might have something to do with the new
Ensembl release.
However, I can't see bacteria_mart_13 from within R:
listMarts()
biomart
version
1 ensembl ENSEMBL
GENES 65 (SANGER UK)
2 snp ENSEMBL
VARIATION 65 (SANGER UK)
3 functional_genomics ENSEMBL
REGULATION 65 (SANGER UK)
4 vega
VEGA 45 (SANGER UK)
5 bacteria_mart_12 ENSEMBL
BACTERIA 12 (EBI UK)
mart=useMart("bacteria_mart_13")
Error in useMart("bacteria_mart_13") :
Incorrect BioMart name, use the listMarts function to see which BioMart
databases are available
Any idea how to get at it from R, or when it will be released?
Cheers,
Gareth
On 03/08/2012 12:14 AM, Dan Staines wrote:
Hi Gareth,
As mentioned in a mail I sent to the list yesterday, we've now released
Ensembl Genomes 13, so bacteria_mart_13 has been retired and is no
longer available through our mart interface. The db is still there on
our public server if you need to use it directly, but there is no change
in the data so I'd suggest you change to use v13 instead.
Best,
Dan Staines.
--
Dan Staines, PhD Ensembl Genomes Technical Coordinator
EMBL-EBI Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
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