Hi, I'm having trouble using biomaRt in mysql mode to access genes from an older human assembly (NCBI35). My query works fine in the web query mode: > ensemblnew<-useMart("ensembl",dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > allgenes<-getBM( c("hgnc_symbol","go","entrezgene"), mart=ensemblnew) > dim(allgenes) [1] 184982 3 but now I'm trying to work with the older assembly, and get the following error with getBM: > ensemblmysql<-useMart ("ensembl_mart_37",dataset="hsapiens_gene_ensembl",archive=T,mysql=T) connected to: ensembl_mart_37 Reading database configuration of: hsapiens_gene_ensembl Checking attributes and filters ... ok Checking main tables ... ok > allgenesmysql<-getBM( c("hgnc_symbol","go_id","entrezgene"), mart=ensemblmysql) Error in exists(filter, martFilters(mart)) : invalid first argument I also tried it with ensembl_mart_47, substituting "go" for "go_id" and it gave the same error. I can't figure out whether I've found a bug, or I'm just doing something wrong. My sessionInfo output is below. I noticed that my RMySQL_0.6-0 is loaded in my session, but not the sessionInfo output given in the vignette (might be using RSQLite_0.6-4 instead) - could that be something to do with it? > sessionInfo() R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.6-0 DBI_0.2-4 biomaRt_1.12.2 RCurl_0.8-3 loaded via a namespace (and not attached): [1] XML_1.93-2 thanks in advance for any help, Janet Young ------------------------------------------------------------------- Dr. Janet Young (Trask lab) Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung at fhcrc.org http://www.fhcrc.org/labs/trask/

Hi Janet, Janet Young wrote: > Hi, > > I'm having trouble using biomaRt in mysql mode to access genes from > an older human assembly (NCBI35). > > My query works fine in the web query mode: > > > ensemblnew<-useMart("ensembl",dataset="hsapiens_gene_ensembl") > Checking attributes and filters ... ok > > allgenes<-getBM( c("hgnc_symbol","go","entrezgene"), mart=ensemblnew) > > dim(allgenes) > [1] 184982 3 > > but now I'm trying to work with the older assembly, and get the > following error with getBM: > > ensemblmysql<-useMart > ("ensembl_mart_37",dataset="hsapiens_gene_ensembl",archive=T,mysql=T) > connected to: ensembl_mart_37 > Reading database configuration of: hsapiens_gene_ensembl > Checking attributes and filters ... ok > Checking main tables ... ok > > allgenesmysql<-getBM( c("hgnc_symbol","go_id","entrezgene"), > mart=ensemblmysql) > Error in exists(filter, martFilters(mart)) : invalid first argument You need to specify a filter and value. Might be a better way to do this but: > mart <- useMart("ensembl_mart_37", "hsapiens_gene_ensembl", archive=T, mysql=T) connected to: ensembl_mart_37 Reading database configuration of: hsapiens_gene_ensembl Checking attributes and filters ... ok Checking main tables ... ok > tmp2 <- getBM(c("hgnc_symbol", "go_id", "entrezgene"),filters="chr_name", values=c(1:24), mart=mart) > dim(tmp2) [1] 177700 3 Lots of <na> in that table -- you might be better off using output="list", but that's up to you. Best, Jim > > I also tried it with ensembl_mart_47, substituting "go" for "go_id" > and it gave the same error. I can't figure out whether I've found a > bug, or I'm just doing something wrong. > > My sessionInfo output is below. I noticed that my RMySQL_0.6-0 is > loaded in my session, but not the sessionInfo output given in the > vignette (might be using RSQLite_0.6-4 instead) - could that be > something to do with it? > > > sessionInfo() > R version 2.6.1 (2007-11-26) > i386-apple-darwin8.10.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RMySQL_0.6-0 DBI_0.2-4 biomaRt_1.12.2 RCurl_0.8-3 > > loaded via a namespace (and not attached): > [1] XML_1.93-2 > > > > thanks in advance for any help, > > Janet Young > > ------------------------------------------------------------------- > Dr. Janet Young (Trask lab) > > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., C3-168, > P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 > email: jayoung at fhcrc.org > > http://www.fhcrc.org/labs/trask/ > > _______________________________________________ > 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 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623