[BioC] biomaRt- too many attributes selected

[Rhoda Kinsella]

Hi Steffen and Lavinia
We have purposely imposed a restriction of three attributes from the  
external section at a time. The main problem was that users were  
selecting too many attributes from this section along with a lot of  
attributes from other sections in the Features attributes and the  
results were not returning. This seemed like the most sensible number  
to allow after some investigation. I am reluctant to change this as it  
has worked for quite a while now and has not caused issues for any  
other users. I will try to do some testing to see if increasing the  
restriction to 4 will cause any problems. If the selection of 4  
external attributes doesn't cause any issues, I will change it in a  
future release.
I hope that helps
Regards
Rhoda


On 3 Jun 2011, at 16:29, Steffen Durinck wrote:

> 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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> <Screen shot 2011-06-03 at 8.24.18 AM.jpg>

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.