Dear BioC, For many months, I have used the GenomeGraphs package without any problems. But since a few days, the following code from the documentation : mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id", biomart = mart) Gives the following error message : error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. I have the following version of R on 64 bit : R version 2.8.1 RC (2008-12-20 r47269) Also, I have installed the release version and development version of GenomeGraphs. Does anyone know what is the problem ? Thanks Arnaud.

Dear Arnaud That is a problem with biomaRt, not GenomeGraphs. I suggest you send the error to the author as something may have changed on the biomart server Regards Michael -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Droit Arnaud Sent: Tue 06/01/2009 4:08 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] GenomeGraphs error Dear BioC, For many months, I have used the GenomeGraphs package without any problems. But since a few days, the following code from the documentation : mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id", biomart = mart) Gives the following error message : error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. I have the following version of R on 64 bit : R version 2.8.1 RC (2008-12-20 r47269) Also, I have installed the release version and development version of GenomeGraphs. Does anyone know what is the problem ? Thanks Arnaud. _______________________________________________ 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

Dear Arnaud thank you for reporting this! There were two issues: 1. GenomeGraphs tries to use the BioMart webservices at Ensembl to query for a property called "biotype" (a.k.a. "structure_biotype"?), which perhaps existed in the past but doesn't seem to be there any more. Steffen Durinck, the author of the GenomeGraphs package, or Rhoda might be able to know better what's going on here. 2. The getBM function produced a slightly obscure error message, which made it difficult to diagnose the error. I have fixed that in the devel version of the biomaRt package. Thank you and best wishes Wolfgang Droit Arnaud ha scritto: > Dear BioC, > > For many months, I have used the GenomeGraphs package without any problems. > But since a few days, the following code from the documentation : > > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id", biomart = mart) > > Gives the following error message : > > error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", : > Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. > > I have the following version of R on 64 bit : R version 2.8.1 RC (2008-12-20 r47269) > Also, I have installed the release version and development version of GenomeGraphs. > > Does anyone know what is the problem ? > > Thanks > > Arnaud.