[BioC] refseq to genesymbol with BiomaRt - problem occurs

Tue Jan 31 14:37:19 CET 2012

Dear Andrea

the same query just worked fine for me (see below), perhaps it is a 
problem with your internet connection (see also the error message that 
you received)?

	Best wishes
	Wolfgang

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

   refseq_mrna hgnc_symbol
1   NM_053017        ART5
                                               description 
chromosome_name  band
1 ADP-ribosyltransferase 5 [Source:HGNC Symbol;Acc:24049] 
11 p15.4
   strand start_position end_position ensembl_gene_id
1     -1        3659733      3663546 ENSG00000167311

On 1/31/12 11:05 AM, andrea.grilli at ior.it wrote:
>
> 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)
> V1
> 1 <!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>ERRORE: La URL richiesta non può essere recuperata</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>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
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber