[BioC] biomaRt and ensembl tables

Wolfgang Huber huber at ebi.ac.uk
Mon Apr 24 14:45:20 CEST 2006

Dear Tabare,

we recommend to use the biomaRt package in the webservice mode. The 
direct access to the Ensembl database tables via MySQL relies one some 
hard coded assumptions which may not apply to the particular table you 
are looking at, also there has recently been a new Ensembl release, 
which might complicate things.

For this reason please use the webservice access to biomarts, which is 
not prone to these problems.

Best wishes
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

TM wrote:
> Hi
> I am having some trouble in using the biomart package.
> I get this error message :
> /Error in mysqlExecStatement(conn, statement, ...) :    RS-DBI driver: 
> (could not run statement: Table 
> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't exist)/
> when executing  this command 
> *getBM(attributes=listAttributes(martMm)[202], 
> filters=listFilters(martMm)[15], values=listT , mart=martMm)
> with 
> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.exon_stable_id_v"
> and **listFilters(martMm)[15] = *
> where martMm has been created this way :* martMm <- useMart(biomart = 
> "ensembl", dataset="mmusculus_gene_ensembl", 
> host="ensembldb.ensembl.org", mysql=TRUE)
> *Can someone help me please
> thank you.

More information about the Bioconductor mailing list