[BioC] biomaRt error

Sonia SHAH S.Shah at cs.ucl.ac.uk
Fri Nov 21 11:51:13 CET 2008


I was carrying out the following biomaRt query:
filter="ensembl_gene_id", value=ids, mart=mart)

and I got the following error:
1 Query ERROR: caught BioMart::Exception::Database: Error during query 
execution: You have an error in your SQL syntax; check the manual that 
corresponds to your MySQL server version for the right syntax to use 
near 'AND main.gene_id_1020_key=ensembl_mart_51.hsapiens_gene_ensembl_
Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", 
"description"),  :
  Number of columns in the query result doesn't equal number of 
attributes in query.  This is probably an internal error, please report.

I don't get errors with queries made to the ENSEMBL 51 VARIATION 
database but get them when using the ENSEMBL 51 GENES database

R version 2.6.1 (2007-11-26)
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] biomaRt_1.14.1 RCurl_0.8-3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 XML_1.93-2

Sonia Shah
Bloomsbury Centre for Bioinformatics
Department of Computer Science
New Engineering Building
Malet Place
London WC1E 6BT

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