Hi John, I just got an email that saying that the BioMart service should be restored now so everything should work at this time. Cheers, Steffen On Wed, Feb 23, 2011 at 11:51 AM, Steffen Durinck <durincks@gene.com> wrote: > Hi John, > > This is a problem at the central BioMart service and needs to be fixed at > their site. > I've contacted them to see what is going on and will let you know as soon > as this is fixed. > > Cheers, > Steffen > > > On Tue, Feb 22, 2011 at 11:20 PM, John Lande <john.lande77@gmail.com>wrote: > >> dear BioC >> >> I still have problem regarding biomart >> >> if I run >> >> > ensembl <- useMart("ensembl") >> > ensembl_human <- useDataset("hsapiens_gene_ensembl", mart=ensembl) >> > EnsTS <- getGene(id = as.vector(TS[,1]), type="entrezgene", >> mart=ensembl_human) >> Error in getBM(attributes = attrib, filters = type, values = id, mart = >> mart) : >> Query ERROR: caught BioMart::Exception::Database: Could not connect to >> mysql database ensembl_mart_61: DBI >> connect('database=ensembl_mart_61;host= >> dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to >> MySQL >> server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ >> biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 >> >> >> I retrieve this error. how can I solve this??? >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]