Jesper Ryge wrote: > thanx laurent :-) > > > ----- Original Message ----- > From: Laurent Gautier <lgautier at="" gmail.com=""> > Date: Monday, December 1, 2008 7:16 pm > Subject: Re: [BioC] Biomart mysql error... > To: Jesper.Ryge at ki.se > Cc: "bioconductor mail list bioconductor at stat.math.ethz.ch" > <bioconductor at="" stat.math.ethz.ch=""> > >> The issue is likely on the server end (updates of the database >> structure). >> I think that sql=TRUE will "only" provide a faster data retrieval. >> >> You can keep=FALSE in the meanwhile. > > hm, could be. but the problem persisted since friday and its still there... i wanted to update > annotation from the whole affy_rat230 chip so its a rather big query and i assume mysql > handle this better... ill brace myself with patience, but should it take so long to correct if its > an error in their end (ensembl database update or something)? does anybody know if this is > the case and when it will be up and running again? In the meanwhile, you may also consider restricting your query to the subset of probesets showing differential expression. L. > cheers, > jesper > >> >> Jesper Ryge wrote: >>> Hi >>> >>> im running into a biomaRt problem when i use the mysql=T in >> useMart which has worked >>> very well earlier on my computer (MacPro3,1 )??? Here is a short >> illustration: >>>> library(biomaRt) >>>> mart <- useMart("ensembl" >> ,dataset="rnorvegicus_gene_ensembl",mysql=T)> connected to: >> ensembl >>> Reading database configuration of: rnorvegicus_gene_ensembl >>> Checking attributes and filters ... ok >>> Checking main tables ... ok >>> >>>> test <- > getBM(attributes=c("ensembl_gene_id","external_gene_id","description "),filters="affy_rat230_ >> 2",values=c("1367452_at","1367453_at"), mart=mart) >>> Error in mysqlExecStatement(conn, statement, ...) : >>> RS-DBI driver: (could not run statement: Table >> 'ensembl_mart_51.ox_AFFY_Rat230_2__dm' >>> doesn't exist) >>> >>> the samme session run with mysql=F works fine! >>> >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-apple-darwin9.5.0 >>> >>> locale: >>> C/UTF-8/C/C/C/C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >> base >>> other attached packages: >>> [1] RMySQL_0.6-1 DBI_0.2-4 biomaRt_1.16.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_0.92-0 XML_1.98-1 >>> >>> any help highly appreciated:-) >>> >>> cheers, >>> jesper Ryge >>> karolinska Institutet >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>

Hi Jesper, biomaRt gets information about tables from an xml description inside the database. It looks like for some reason the table that biomaRt associates with the rat chip is incorrect. I'll investigate and fix it if the problem is at the biomaRt side. Your query shouldn't be slow when you set mysql=F. The BioMart webservices are pretty fast. Setting mysql=F is the preferred way to use biomaRt as it is better supported by the BioMart developers and relies less on the query building we do on the R side with mysql=T (which is harder to maintain when things change in new Ensembl releases). Cheers, Steffen > thanx laurent :-) > > > ----- Original Message ----- > From: Laurent Gautier <lgautier at="" gmail.com=""> > Date: Monday, December 1, 2008 7:16 pm > Subject: Re: [BioC] Biomart mysql error... > To: Jesper.Ryge at ki.se > Cc: "bioconductor mail list bioconductor at stat.math.ethz.ch" > <bioconductor at="" stat.math.ethz.ch=""> > >> >> The issue is likely on the server end (updates of the database >> structure). >> I think that sql=TRUE will "only" provide a faster data retrieval. >> >> You can keep=FALSE in the meanwhile. > > hm, could be. but the problem persisted since friday and its still > there... i wanted to update > annotation from the whole affy_rat230 chip so its a rather big query and i > assume mysql > handle this better... ill brace myself with patience, but should it take > so long to correct if its > an error in their end (ensembl database update or something)? does anybody > know if this is > the case and when it will be up and running again? > > cheers, > jesper > >> >> >> Jesper Ryge wrote: >> > Hi >> > >> > im running into a biomaRt problem when i use the mysql=T in >> useMart which has worked >> > very well earlier on my computer (MacPro3,1 )??? Here is a short >> illustration: >> > >> >> library(biomaRt) >> > >> >> mart <- useMart("ensembl" >> ,dataset="rnorvegicus_gene_ensembl",mysql=T)> connected to: >> ensembl >> > Reading database configuration of: rnorvegicus_gene_ensembl >> > Checking attributes and filters ... ok >> > Checking main tables ... ok >> > >> >> test <- >> > >> > getBM(attributes=c("ensembl_gene_id","external_gene_id","description "),filters="affy_rat230_ >> 2",values=c("1367452_at","1367453_at"), mart=mart) >> > Error in mysqlExecStatement(conn, statement, ...) : >> > RS-DBI driver: (could not run statement: Table >> 'ensembl_mart_51.ox_AFFY_Rat230_2__dm' >> > doesn't exist) >> > >> > the samme session run with mysql=F works fine! >> > >> >> sessionInfo() >> > R version 2.8.0 (2008-10-20) >> > i386-apple-darwin9.5.0 >> > >> > locale: >> > C/UTF-8/C/C/C/C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods >> base >> > >> > other attached packages: >> > [1] RMySQL_0.6-1 DBI_0.2-4 biomaRt_1.16.0 >> > >> > loaded via a namespace (and not attached): >> > [1] RCurl_0.92-0 XML_1.98-1 >> > >> > any help highly appreciated:-) >> > >> > cheers, >> > jesper Ryge >> > karolinska Institutet >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >