[BioC] refseq to genesymbol with BiomaRt - problem occurs

Tue Jan 31 11:05:23 CET 2012

Dear list,
I need to convert refseq ID to genesymbol. I used biomaRt but I get  
this error:

> library(biomaRt)
> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> getGene(id = "NM_053017", type = "refseq_mrna", mart = mart)

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2                                             <HTML><HEAD><META  
HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3                                                     <TITLE>ERRORE:  
La URL richiesta non può essere recuperata</TITLE>
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type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
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                                         <H1>ERRORE</H1>
Error in getBM(attributes = attrib, filters = type, values = id, mart  
= mart) :
   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.

In fact I need to process a vector of refseq id with the following  
code but I get same error as before:
> getGene(id = table[,1], type = "refseq_mrna", mart = mart)

Changing the id type (e.g. refseq_dna) doesn't change the result. Is  
it my input error or some problem with biomaRt package occurred?
Thanks in advance,
Andrea

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] annotate_1.32.0       biomaRt_2.10.0        annaffy_1.26.0
  [4] KEGG.db_2.6.1         GO.db_2.6.1           hgu133plus2.db_2.6.3
  [7] org.Hs.eg.db_2.6.4    RSQLite_0.11.1        DBI_0.2-5
[10] AnnotationDbi_1.16.10 Biobase_2.14.0

loaded via a namespace (and not attached):
[1] IRanges_1.12.5 RCurl_1.8-0    tools_2.14.0   XML_3.6-2      xtable_1.6-0