[BioC] non-BiomaRt die

Waqasuddin Khan [guest] guest at bioconductor.org
Sat Jan 25 03:42:06 CET 2014

I tried to retrieve ensembl_gene_id and go_term for my arabidopsis thaliana gene from my gene_name list:
> head(gene_name)
1         ANAC001
2            DCL1
3         MIR838A
4       AT1G01073
5           IQD18
6       AT1G01115

> unimart = useMart("plants_mart_20",dataset="athaliana_eg_gene")

> getBM(attributes=c("ensembl_gene_id", "go_accession"),filters=c("ensembl_gene_id"),values=gene_name,mart=unimart)

but got the folloeing error? I did not figure it out? is it an error from my side or from the biomart server?

 -- output of sessionInfo(): 

Error in getBM(attributes = c("ensembl_gene_id", "go_accession"), filters = c("ensembl_gene_id"),  : 
  Query ERROR: caught BioMart::Exception: non-BioMart die(): 
not well-formed (invalid token) at line 1, column 21728, byte 21728 at /usr/lib/perl5/XML/Parser.pm line 187

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