[BioC] Biomart server down?

Rhoda Kinsella rhoda at ebi.ac.uk
Fri May 20 17:18:49 CEST 2011


Hi Fabrice
Unfortunately we have never been able to have a functional count for  
the regulation mart as restrictions in the 0.7 Biomart code as well as  
the complexity of the regulation schema does not allow it. The rest of  
the mart does work as expected.
Regards
Rhoda


On 20 May 2011, at 16:08, Fabrice Tourre wrote:

> 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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> 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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.



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