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: >> >> >> >> <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 >>> >>> >>> >>> ______________________________________________________________________ >>> This email has been scanned by the MessageLabs Email Security System. >>> For more information please visit http://www.messagelabs.com/email >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> <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. > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > If you have any question, please contact MCRI IT Helpdesk for further > assistance. > ______________________________________________________________________ -- Senior Bioinformatics Officer Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. 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