[BioC] BiomaRt Query error Edited

Tue Jun 5 13:56:17 CEST 2012

My apologies. I omitted the "error" in my initial post.

Hi all,

I ran a list of genes through biomaRt with the following code and it
gives me this error in the snp retrieval aspect of it. I doubt it's a
connection/proxy problem because I have that taken care of, I think
and every step prior to that seemed to have worked just fine.

Any ideas what the problem might be?

Thanks.

-Avoks

mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
genes = read.delim("DAVID_BFE_Genes_4_06_2012.txt", header = TRUE)
results = getBM(attributes = c("ensembl_gene_id", "hgnc_symbol",
"chromosome_name","strand", "transcript_start", "transcript_end" ),
filters = "hgnc_symbol", values = genes$Symbol, mart = mart)
mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
results2 = getBM(attributes = c("refsnp_id", "allele", "snp",
       "chrom_strand", "cds_start","cds_end","validated",
       "consequence_type_tv","phenotype_name"),
       filters = "ensembl_gene", values = results$ensembl_gene_id, mart = mart2)

<!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN
http://www.w3.org/TR/html4/loose.dtd>
2                                             <HTML><HEAD><META
HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3
<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
4 <STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
5
                                          </HEAD><BODY>
6
                                         <H1>ERROR</H1>
Error in getBM(attributes = c("refsnp_id", "allele", "snp", "chrom_strand",  :
  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.
>

 sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_1252  LC_CTYPE=English_.1252
[3] LC_MONETARY=English_.1252 LC_NUMERIC=C
[5] LC_TIME=English_.1252

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

other attached packages:
[1] BiocInstaller_1.4.6 biomaRt_2.12.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
>