This is indeed a BioMart server side issue and there is nothing we can try on the biomaRt end to fix it. The plant_mart is maintained by Ensembl so you could report this to helpdesk@ensembl.org or leave a message here: http://plants.ensembl.org/Help/Contact Cheers, Steffen On Wed, Feb 2, 2011 at 6:54 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > Maybe I'm missing something, but everything about the scenario you > describe (especially since you are getting errors via their website) > seems to suggest that this is a problem on the biomart side, right? > > Perhaps you should try contacting them to let them now? > > Sorry if I misunderstood. > -steve > > On Wed, Feb 2, 2011 at 3:03 AM, Ying Zhu <ying.zhu@csiro.au> wrote: > > Dear Folks, > > > > I encountered a problem with Biomart Query via getBM function in biomaRt > package. > > > >>mart <- useMart("plant_mart_7") > > +mart<-useDataset("vvinifera_eg_gene",mart) > > > +getBM(attributes=c("affy_vitis_vinifera","go_molecular_function_id" ,"entrezgene"),filters="affy_grape", > +values=c("1616932_at","1608265_at","1614550_at","1608133_at","16184 59_at"), > mart=mart) > > Checking attributes ... ok > > Checking filters ... ok > > Error in getBM(attributes = c("affy_vitis_vinifera", > "go_molecular_function_id", : > > Query ERROR: caught BioMart::Exception::Database: Error during query > execution: Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist > > > > And it's the same error when using web query of > http://www.biomart.org/biomart/marview/ > > > > Serious Error: Error during query execution: Table > 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist > > ERROR: caught BioMart::Exception::Database: Error during query execution: > Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist > > > > I checked this configuration page: > http://www.biomart.org/biomart/martservice?type=configuration&datase t=vvinifera_eg_gene > > Two different parameters were found, and I reckon the first was wrong. > > tableConstraint="efg_affy_vitis_vinifera__dm" > > tableConstraint="vvinifera_eg_gene__efg_affy_vitis_vinifera__dm" > > It's obvious that the error happened in "martservice" web server. > > As the file is on the www.biomat.org server, is it possible to fix that > within biomaRt package in R? > > Or what do you think is the root problem? I might be wrong to some > extent. > > Thanks a lot in advance for anyone could be of kind help and make any > suggestions. > > =================================================== > > Cordially yours, > > Ying Zhu > > PostDoctoral Fellow, CSIRO Plant Industry, Adelaide Laboratory > > Wine Innovation West Building, Hartley Grove, Urrbrae SA > > PO Box 350, Glen Osmond SA 5064, Australia > > Facsimile: +61 8 8303 8601 > > Cellphone: +61 4 0121 3248 > > > > > > [[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 > > > > > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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]]