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]]

