[BioC] biomaRt- too many attributes selected

[Lavinia Gordon]

Hi Steffen and Rhoda,

Thank you so much for following this up.
I can see that three makes sense, as I am sure that the amount of data 
returned can easily become enormous.  It is a pity though because it is 
nice to know *everything* about your genes of interest!

Many thanks,

Lavinia.

On 4/06/2011 2:07 AM, Rhoda Kinsella wrote:
> 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.
>
>
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-- 
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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