[BioC] biomaRt query problems- plants_mart_10

Sun Oct 23 23:32:14 CEST 2011

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