[BioC] Biomart server down?

Fri May 20 16:58:01 CEST 2011

Hi Alistair
You can set your host to www.ensembl.org and use the Ensembl Biomart  
databases there.
Regards
Rhoda

On 20 May 2011, at 15:44, Alistair Rust wrote:

> Hi,
>
> I've had an R script playing nicely with biomaRt for a while
> Today there seem to be a few wee problems.  Is the result
> of the server being down in Toronto?
>
> SessionInfo, a simple test and output below.  I downloaded
> and installed the 2.8.0 version of biomaRt this morning.
> Also tried the 2.9.0 development version with the same
> results.
>
> Cheers
>
> Alistair
>
> Team113: Experimental Cancer Genetics,
> Wellcome Trust Sanger Institute,
> Hinxton, Cambridge, UK
>
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=C
> [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.8.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-2 XML_3.1-0
>
>
> Simple test from the R script on the BioConductor biomaRt webpage
> ========
> library(biomaRt)
>
> listMarts()
>
> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
>
> affyids=c("202763_at","209310_s_at","207500_at")
>
> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters =
> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl)
> =========
>
>
>
> Output
> =========
>
>      V1
>
> 1 <!DOCTYPE html PUBLIC -//W3C//DTD HTML 4.01//EN
> http://www.w3.org/TR/html4/strict.dtd>
> 2
> <html><head>
> 3                        <meta http-equiv=Content-Type content=text/ 
> html;
> charset=utf-8>
> 4                         <title>ERROR: The requested URL could not be
> retrieved</title>
> 5                                                             <style
> type=text/css><!--
> 6
> /*
> Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"),  
> filters
> = "affy_hg_u133_plus_2",  :
>  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.
>
> 	[[alternative HTML version deleted]]
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.