[BioC] biomart error returning data

Tue May 29 10:17:47 CEST 2012

Hello

I ran the below commands and got an error. The output asked me to post to the list so here it is. 

a similar problem was reported for a different related database query:
http://article.gmane.org/gmane.science.biology.informatics.conductor/25233/match=biomart+invalid+result

I will go about it in an different way I think

thanks

Alasdair

 -- output of sessionInfo(): 

> M1_0.exprs = read.table("M1_0.txt", sep="\t", header=TRUE)
> library(biomaRt)
> ensembl.mart = useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl")
> ensembl.gene.pos = getBM(attributes = c("ensembl_gene_id","chromosome_name","start_position","end_position"), filters = "ensembl_gene_id", values = rownames(M1_0.exprs), mart = ensembl.mart)
                                                                                                                            V1
1                           <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd>
2                                             <HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3                                                               <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
4 <STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
5                                                                                                                </HEAD><BODY>
6                                                                                                               <H1>ERROR</H1>
Error in getBM(attributes = c("ensembl_gene_id", "chromosome_name", "start_position",  : 
  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 2.15.0 (2012-03-30)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] biomaRt_2.12.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 tools_2.15.0 XML_3.9-4  

> traceback()
2: stop("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.")
1: getBM(attributes = c("ensembl_gene_id", "chromosome_name", "start_position", 
       "end_position"), filters = "ensembl_gene_id", values = rownames(data), 
       mart = ensembl.mart)

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