Indeed that seems to be the problem. Cheers, Steffen > Hi Steffen and Elizabeth, > I have had a look through the ensembl mart configuration and have > found an error which may fix the current gene and transcript biotype > problem. > The pointer attribute for the structure_biotype is still pointing to > biotype so I will change this to point to gene_biotype and this should > solve the issue. I will > implement this change for release 53 (approximately mid February). My > apologies for any inconvenience and thank you for reporting this > problem. > Regards, > Rhoda > > > On 13 Jan 2009, at 10:08, Rhoda Kinsella wrote: > >> Hi Steffen and Elizabeth, >> The biotype attribute was changed into gene_biotype and >> transcript_biotype after a user requested that >> we provide the transcript_biotype information. I have carried out >> the query below on the Ensembl mart web interface and >> there are no errors reported. Steffan, can you provide me with some >> more information about where you think >> the source of the problem is and I can help look into this? >> Kind regards, >> Rhoda >> >> >> >> >> On 12 Jan 2009, at 20:48, steffen at stat.berkeley.edu wrote: >> >>> Hi Elizabeth, >>> >>> The biotype attribute seem to have changed into a separate >>> gene_biotype >>> and transcript_biotype these two represent the same info. >>> >>> These two new attributes however are indeed currently not >>> retrievable and >>> I am investigating what causes this. It looks like it is on the >>> BioMart >>> side. >>> >>> Cheers, >>> Steffen >>> >>> >>> >>>> Hi, >>>> I am trying to pull down information from Ensembl using biomaRt >>>> and I >>>> can't get the relevant biotype information (for Human). The old >>>> 'biotype' attribute doesn't exist, so what I see is 'gene_biotype' >>>> and >>>> 'structure_biotype'. I have no idea what the difference is, but I >>>> can't >>>> get either one. The error says it's probably an internal error to be >>>> reported, but I also get this when I try to bring down what I >>>> think are >>>> incompatible attributes. >>>> Thanks, >>>> Elizabeth >>>> >>>>> library(biomaRt) >>>>> mart<-useMart("ensembl",dataset= "hsapiens_gene_ensembl") >>>> Checking attributes and filters ... ok >>>>> martAttr<-listAttributes(mart) >>>>> att<-c("ensembl_gene_id", >>>> + "ensembl_transcript_id", >>>> + "ensembl_exon_id", >>>> + "exon_chrom_start", >>>> + "exon_chrom_end", >>>> + "strand", >>>> + "chromosome_name", >>>> + "rank", >>>> + "3_utr_start","3_utr_end", >>>> + "5_utr_start","5_utr_end" >>>> + ) >>>>> all(att%in%martAttr[,1]) #valid names for the mart >>>> [1] TRUE >>>> #works fine here >>>>> tempGene <- >>>> getBM(att,filter="ensembl_gene_id",value="ENSG00000187634",mart = >>>> mart) >>>> #error >>>>> tempGene <- >>>> getBM >>>> (c >>>> (att >>>> ,"gene_biotype >>>> "),filter="ensembl_gene_id",value="ENSG00000187634",mart >>>> = mart) >>>> >>>> V1 >>>> 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from >>>> multiple attribute pages are not allowed >>>> Error in getBM(c(att, "gene_biotype"), filter = "ensembl_gene_id", >>>> value >>>> = "ENSG00000187634", : >>>> Number of columns in the query result doesn't equal number of >>>> attributes in query. This is probably an internal error, please >>>> report. >>>> #again an error >>>>> tempGene <- >>>> getBM >>>> (c >>>> (att >>>> ,"structure_biotype >>>> "),filter="ensembl_gene_id",value="ENSG00000187634",mart >>>> = mart) >>>> >>>> V1 >>>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype >>>> NOT >>>> FOUND >>>> Error in getBM(c(att, "structure_biotype"), filter = >>>> "ensembl_gene_id", : >>>> Number of columns in the query result doesn't equal number of >>>> attributes in query. This is probably an internal error, please >>>> report. >>>>> sessionInfo() >>>> R version 2.8.1 (2008-12-22) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>> States.1252;LC_MONETARY=English_United >>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] biomaRt_1.16.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_0.93-0 tools_2.8.1 XML_1.99-0 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> _______________________________________________ >>> 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 >> >> Rhoda Kinsella Ph.D. >> Ensembl Bioinformatician, >> European Bioinformatics Institute (EMBL-EBI), >> Wellcome Trust Genome Campus, >> Hinxton >> Cambridge CB10 1SD, >> UK. >> >> _______________________________________________ >> 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 > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. >