[BioC] BiomaRt getBM error: Unknown column
Yury Bukhman [guest]
guest at bioconductor.org
Mon Apr 7 17:03:29 CEST 2014
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_transcript"),mart=bdi.genes.dataset,verbose=T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><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
>
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