Hello, For some reason, biomaRt is sometimes misbehaving when the query results have empty fields. Without returning NA, it fails the whole query. >library(biomaRt) >ensembl = useMart("ensembl", dataset="mmusculus_gene_ensembl") #if I ask for an entrezgene id, it does not work > getBM (attributes = c ("ensembl_transcript_id ","entrezgene","description"),filters="ensembl_transcript_id", values="ENSMUST00000005400", mart=ensembl) [1] ensembl_transcript_id entrezgene description <0 rows> (or 0-length row.names) #if I leave out the entrezgene field, it works > getBM (attributes = c ("ensembl_transcript_id ","description"),filters="ensembl_transcript_id", values="ENSMUST00000005400", mart=ensembl) ensembl_transcript_id 1 ENSMUST00000005400 description 1 prolactin receptor Gene [Source:MGI Symbol;Acc:MGI:97763] > sessionInfo() R version 2.11.0 (2010-04-22) i386-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.4.0 R.utils_1.4.0 R.oo_1.7.2 R.methodsS3_1.2.0 [5] Biobase_2.7.4 loaded via a namespace (and not attached): [1] affy_1.25.2 affyio_1.15.2 limma_3.3.10 [4] marray_1.25.1 preprocessCore_1.9.0 RCurl_1.3-1 [7] tools_2.11.0 XML_2.8-1 Does anyone have an idea why this might be hapening? Cheers, Nenad Bartonicek Nenad Bartonicek PhD student, Enright group European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom tel: +44-755-435-9057 [[alternative HTML version deleted]]

Hi Nenad, Thanks for reporting this. It looks like the BioMart web-interface at www.ensembl.org/biomart produces the same error. So the error is upstream of the biomaRt package. I'll contact the ensembl helpdesk to make them aware of this issue and we can have a fix soon. Cheers, Steffen On 4/28/10, Nenad Bartonicek <nenad at="" ebi.ac.uk=""> wrote: > Hello, > > For some reason, biomaRt is sometimes misbehaving when the query > results have empty fields. Without returning NA, it fails the whole > query. > > >library(biomaRt) > >ensembl = useMart("ensembl", dataset="mmusculus_gene_ensembl") > > #if I ask for an entrezgene id, it does not work > > > getBM > (attributes > = > c > ("ensembl_transcript_id > ","entrezgene","description"),filters="ensembl_transcript_id", > values="ENSMUST00000005400", mart=ensembl) > > [1] ensembl_transcript_id entrezgene description > <0 rows> (or 0-length row.names) > > #if I leave out the entrezgene field, it works > > > getBM > (attributes > = > c > ("ensembl_transcript_id > ","description"),filters="ensembl_transcript_id", > values="ENSMUST00000005400", mart=ensembl) > > ensembl_transcript_id > 1 ENSMUST00000005400 > description > 1 prolactin receptor Gene [Source:MGI Symbol;Acc:MGI:97763] > > > sessionInfo() > R version 2.11.0 (2010-04-22) > i386-apple-darwin9.8.0 > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] biomaRt_2.4.0 R.utils_1.4.0 R.oo_1.7.2 > R.methodsS3_1.2.0 > [5] Biobase_2.7.4 > > loaded via a namespace (and not attached): > [1] affy_1.25.2 affyio_1.15.2 limma_3.3.10 > [4] marray_1.25.1 preprocessCore_1.9.0 RCurl_1.3-1 > [7] tools_2.11.0 XML_2.8-1 > > > Does anyone have an idea why this might be hapening? > > Cheers, > > Nenad Bartonicek > > Nenad Bartonicek > PhD student, Enright group > European Bioinformatics Institute > Hinxton > Cambridge > CB10 1SD > United Kingdom > tel: +44-755-435-9057 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >