[BioC] biomaRt- too many attributes selected
lavinia.gordon at mcri.edu.au
Mon Jun 6 07:40:23 CEST 2011
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!
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
> 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" />
>> 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
>>> 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
>>> for External References
>>> where myattributes =
>>>  "mim_morbid_accession" "mim_morbid_description"
>>> and entrez =
>>>  "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.
>>> R version 2.12.0 (2010-10-15)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
>>> LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>>> attached base packages:
>>>  stats graphics grDevices utils datasets methods base
>>> other attached packages:
>>>  biomaRt_2.6.0 limma_3.6.9
>>> 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):
>>>  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
>>> Senior Bioinformatics Officer
>>> Murdoch Childrens Research Institute
>>> Royal Children's Hospital
>>> Flemington Road
>>> Victoria 3052
>>> This email has been scanned by the MessageLabs Email Security System.
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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,
> Cambridge CB10 1SD,
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Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
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