[BioC] biomaRt query problems- plants_mart_10

Sat Oct 22 14:34:22 CEST 2011

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