[BioC] BiomaRt getBM error: Unknown column

[Yury Bukhman [guest]]

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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