[BioC] BioMart Error

[Wolfgang Huber]

Hi Lakshmanan

thank you for reporting this and apologies for the delayed reply. It 
turns out that there is a disagreement about the format of the data 
reported from the SNP biomart webservice that you are querying and the 
biomaRt R package.

Resolving this seems to be a complex and slow procedure. For the time 
being, please do not use biomaRt with the SNP biomart, it will not work.

Best wishes
      Wolfgang

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

> -------- Original Message --------
> Subject: [BioC] BioMart Error
> Date: Fri, 4 Sep 2009 10:54:19 -0400
> From: Lakshmanan Iyer <laxvid at gmail.com>
> To: Bioconductor at stat.math.ethz.ch
> 
> Hi,
> I Ran the following code and it did not work and asked me to report the
> error to the list. So here it is:
> ### Code####
> library (biomaRt);
> snps <- useMart("snp", dataset="hsapiens_snp");
> filters <- listFilters(snps);
> attributes <- listAttributes(snps);
> #
> required_attributes <- attributes[,1]
> required_list <- c("ENSG00000006638" ,"ENSG00000110148");
> i22 <- getBM(  attributes=required_attributes[30:45],
> filters="ensembl_gene", values=required_list, mart=snps)
> ### Code End ###
> 
> and got the following error:
>>>>>>>>>>>>>>
> Error in getBM(attributes = required_attributes[30:45], filters =
> "ensembl_gene",  :
>   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 2.9.0 (2009-04-17)
> i486-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.0.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.97-3 XML_2.3-0
> 
> -Best
> -Lax
> 
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> 
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