[BioC] biomaRt- too many attributes selected

[Steffen Durinck]

Hi Lavinia,

This is indeed a bit strange and is possibly due to a setting of the
Ensembl BioMart.  I CC'd Rhoda or Ensembl to check if this can be
resolved at the Ensembl side.
When you do the same query using the web interface, one gets the same
error, see screenshot in attach.
For now you'll have to do two queries to get the results.

Rhoda, the query we are trying is:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0"
uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
			
	<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Filter name = "entrezgene" value = "673,837"/>
		<Attribute name = "mim_morbid_accession" />
		<Attribute name = "mim_morbid_description" />
		<Attribute name = "mim_gene_accession" />
		<Attribute name = "mim_gene_description" />
	</Dataset>
</Query>


Cheers,
Steffen

On Thu, Jun 2, 2011 at 7:07 PM, Lavinia Gordon
<lavinia.gordon at mcri.edu.au> wrote:
> Dear biomaRt users,
>
> Following a simple query like Task 2 in the biomaRt users guide
> (http://bioconductor.org/packages/2.8/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf),
>
> getBM(attributes = myattributes, filters = "entrezgene", values =
> entrez,mart = ensembl)
>
> I am running into an issue with this error:
> Error in getBM(attributes = myattributes, filters = "entrezgene", values =
> entrez,  :
>  Query ERROR: caught BioMart::Exception::Usage: Too many attributes selected
> for External References
>
> where myattributes =
> [1] "mim_morbid_accession"   "mim_morbid_description" "mim_gene_accession"
>   "mim_gene_description"
>
> and entrez =
> [1] "673" "837"
>
> Is there anyway around this error rather than just running two queries? I am
> surprised that four attributes are considered too many.
>
> With thanks for your help,
>
> Lavinia Gordon.
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>  LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.6.0          limma_3.6.9            hgu133plus2probe_2.7.0
> AnnotationDbi_1.12.0   hgu133plus2cdf_2.7.0   gcrma_2.22.0
> affy_1.28.0            Biobase_2.10.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.18.0         Biostrings_2.18.4     DBI_0.2-5
> IRanges_1.8.9         preprocessCore_1.12.0 RCurl_1.5-0.1
> RSQLite_0.9-4         splines_2.12.0        tools_2.12.0
>  XML_3.2-0.2
>
>
> --
> Senior Bioinformatics Officer
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road
> Parkville
> Victoria 3052
> Australia
> www.mcri.edu.au
>
>
>
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