[BioC] Biomart server down?

Fri May 20 17:08:03 CEST 2011

On website http://www.ensembl.org/biomart/martview/a711f46360c68acaec88385696d09186/a711f46360c68acaec88385696d09186

I want to get the REGULATORY FEATURES

It seems not work.

Dataset Count unavailable

On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
> 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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
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> Search the archives:
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>