Cheers Dan, I'll see if I can figure out how to do that. I'm a bit of an R newbie (or to be honest a complete beginner at all things bioinformatic), but that should be possible in theory, I guess. I'll post a fix if I can make something work. Thanks, Gareth
On 8 Mar 2012, at 23:03, Dan Staines wrote: > 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/ _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
