[BioC] biomaRt query problems- plants_mart_10

Sun Oct 23 23:27:44 CEST 2011

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.

	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