[ensembl-dev] problems when querying properties of ENSDARG00000077431

[Holger Brandl]

Hi,

when I execute the following bits in R (2.13) I get an error:

library(biomaRt)
mart = useDataset("drerio_gene_ensembl", mart = useMart("ensembl"))
getBM(attributes=c('ensembl_gene_id', 'gene_exon_intron', 'external_gene_id'), 
filters=c('ensembl_gene_id'), values="ENSDARG00000077431", mart=mart);

The error message is:
Error in getBM(attributes = c("ensembl_gene_id", "gene_exon_intron", 
"external_gene_id"),  :
   The query to the BioMart webservice returned an invalid result: the number of 
columns in the result table does not equal the number of attributes in the 
query. Please report this to the mailing list.


The same query works fine for all other genes I've tried. The problem might be 
related to the missing external_gene_id for ENSDARG00000077431 in the enesembl 
database, because the query works nicely when I remove it from the list of 
attributes.

Here's my session info:
>  sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  grid      methods   base

other attached packages:
[1] biomaRt_2.7.2 stringr_0.5   ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 
plyr_1.5.2

loaded via a namespace (and not attached):
[1] RCurl_1.6-6 XML_3.4-0


Best, Holger Brandl

-- 
Dr. Holger Brandl
Bioinformatics Service
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden, Germany

Tel.:   +49/351/210-2738
Fax:    +49 351 210 2000
www:  http://www.mpi-cbg.de