BiomaRt getBM error: Unknown column
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Hi, I am trying to use BiomaRt to convert ENTREZ gene ids to the corresponding JGI ids in Brachipodium distachyon. getBM fails, apparently because it can't find a column in a database. Here are my commands and outputs: > library(biomaRt) > x = listMarts() > grep("PLANTS",x$biomart,value=T,ignore.case=T) [1] "plants_mart_21" "plants_variations_21" > mart = useMart("plants_mart_21") > grep("bdist",listDatasets(mart)$dataset,value=T) [1] "bdistachyon_eg_gene" > bdi.genes.dataset = useDataset("bdistachyon_eg_gene",mart=mart) > > attrs = listAttributes(bdi.genes.dataset) > attrs[grep("entrez",attrs$name),] name description 22 entrezgene EntrezGene ID > attrs[grep("jgi",attrs$name),] name description 25 jgi_gene JGI gene ID 26 jgi_transcript JGI transcript ID > > entrez2jgi = getBM(attributes=c("entrezgene","jgi_gene","jgi_transcr ipt"),mart=bdi.genes.dataset,verbose=T) <query virtualschemaname="default" uniquerows="1" count="0" datasetconfigversion="0.6" header="0" requestid="biomaRt"> <dataset name="bdistachyon_eg_gene"><attribute name="entrezgene"/><attribute name="jgi_gene"/><attribute name="jgi_transcript"/></dataset></query> ################# Results from server: [1] "Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'plants_mart_21.bdistachyon_eg_gene__ox_entrezgene__dm.translatio' in 'where clause'\n" attr(,"Content-Type") "text/plain" Error in getBM(attributes = c("entrezgene", "jgi_gene", "jgi_transcript"), : Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'plants_mart_21.bdistachyon_eg_gene__ox_entrezgene__dm.translatio' in 'where clause' I am using the current versions of R and Bioconductor, afaik: > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite("BiocUpgrade") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3. Warning message: Bioconductor version 2.13 is the latest available for R version 3.0.0 > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3. > library(BiocInstaller) > biocValid() [1] TRUE -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.18.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 tools_3.0.3 XML_3.98-1.1 > -- Sent via the guest posting facility at bioconductor.org.
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