[BioC] biomaRt query problems- plants_mart_10
Samuel Wuest
wuests at tcd.ie
Mon Oct 24 10:13:05 CEST 2011
Oh, I am sorry, haven't seen the announcement.
My queries are working again, so back to normal.
Thanks a lot! Sam
On 23 October 2011 22:32, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Sun, Oct 23, 2011 at 2:27 PM, Wolfgang Huber <whuber at embl.de> wrote:
>> Dear Sam
>>
>> I have just run your script, and it seemed to work fine. Session info and
>> output are below.
>>
>> Looking at your error message: "Information Systems Services - Trinity
>> College Dublin - Access error 503" it does look like a problem with your
>> local configuration at TCD.
>>
>
> It could also be the scheduled downtime for the biomart servers,
> please see the announcement here:
>
> https://stat.ethz.ch/pipermail/bioconductor/2011-October/041685.html
>
> Dan
>
>
>> Best wishes
>> Wolfgang
>>
>>> str(retr.data)
>> 'data.frame': 21 obs. of 5 variables:
>> $ ensembl_gene_id : chr "AT1G01060" "AT1G01060" ...
>> $ ensembl_transcript_id : chr "AT1G01060.3" "AT1G01060.5" ...
>> $ ensembl_peptide_id : chr "AT1G01060.3" "AT1G01060.5" ...
>> $ canonical_transcript_stable_id: chr "AT1G01060.3" "AT1G01060.3" ...
>> $ description : chr "Homeodomain-like superfamily
>> protein.[Source:TAIR;Acc:AT1G01060]" ...
>>
>>> sessionInfo()
>> R Under development (unstable) (2011-10-23 r57407)
>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] biomaRt_2.9.3 org.At.tair.db_2.6.4 RSQLite_0.10.0
>> [4] DBI_0.2-5 AnnotationDbi_1.15.40 Biobase_2.13.11
>> [7] BiocInstaller_1.1.29 fortunes_1.4-2
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.11.31 RCurl_1.6-10 XML_3.4-3 tools_2.15.0
>>
>>
>>
>> Oct/22/11 2:34 PM, Samuel Wuest scripsit::
>>>
>>> Hi,
>>>
>>> I have tried to use biomaRt (primarily for use in the
>>> GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart,
>>> and it seems that the service is unstable at the moment (that is, it
>>> works in times but not others). I observed the problem firstly two
>>> days ago and I have not been able to connect today...
>>>
>>> Below, I have included some example code to demonstrate the error. I
>>> have read a similar post on the topic, where the problems seemed to
>>> have been at the server-side and not the user-side (?).
>>>
>>> Any suggestions, in case I have to troubleshoot on my side?
>>>
>>> Thanks a lot for any help.
>>>
>>> Best, Sam
>>>
>>>
>>>> library(org.At.tair.db)
>>>> library(biomaRt)
>>>>
>>>> myMart<- useMart("plants_mart_10", dataset="athaliana_eg_gene")
>>>>
>>>> genes<- ls(org.At.tairSYMBOL)[1:10]
>>>> att<- listAttributes(myMart)[1:5,1]
>>>> filt<- "tair_locus"
>>>>
>>>> retr.data<- getBM(att, filt, values=genes, myMart)
>>>
>>> V1
>>> 1<!DOCTYPE html PUBLIC -//W3C//DTD XHTML 1.0 Transitional//EN
>>> http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd>
>>> 2<html
>>> xmlns=http://www.w3.org/1999/xhtml xml:lang=en lang=en>
>>> 3
>>> <head>
>>> 4<title>Information Systems Services -
>>> Trinity College Dublin - Access error 503</title>
>>> 5<meta
>>> http-equiv=Content-Type content=text/html; charset=iso-8859-1 />
>>> 6<meta name=keywords content=trinity college dublin,
>>> trinity, university of dublin, university, ireland />
>>> Error in getBM(att, filt, values = genes, myMart) :
>>> 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.
>>>>
>>>> sessionInfo()
>>>
>>> R version 2.13.0 (2011-04-13)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] biomaRt_2.8.0 org.At.tair.db_2.5.0 RSQLite_0.9-4
>>> DBI_0.2-5 AnnotationDbi_1.14.1 Biobase_2.12.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_1.5-0 XML_3.4-0
>>>
>>> -------------------------------------------------------
>>> Samuel Wuest
>>> Smurfit Institute of Genetics
>>> Trinity College Dublin
>>> Dublin 2, Ireland
>>> Phone: +353-1-896 2444
>>> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
>>> Email: wuests at tcd.ie
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> --
>>
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>> _______________________________________________
>> Bioconductor mailing list
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>>
>
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>
--
-----------------------------------------------------
Samuel Wuest
Smurfit Institute of Genetics
Trinity College Dublin
Dublin 2, Ireland
Phone: +353-1-896 2444
Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
Email: wuests at tcd.ie
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