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Dear Galina, Where did you get the Ensembl gene identifiers from? It looks like they are not present in Ensembl and this is why getBM returns NULL. Are you sure the identifiers are correct and have the right amount of 0's in them? e.g. ENSG00000008311 does return data. Cheers, Steffen Glazko, Galina wrote: > Dear list, > > > > I am trying to do very simple query using BiomaRt: > > library(biomaRt) > > ensembl=useMart('ensembl') > > ensembl= useDataset('hsapiens_gene_ensembl',mart=ensembl) > > .. > > >> ids<-c("ENSG000000282326","ENSG000000008311","ENSG000000323881") >> > > >> hsdef <- >> > getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","hgnc_s ymbo > l"),filters="ensembl_gene_id",values=ids, mart=ensembl) > > >> hsdef >> > > NULL > > > > Please let me know, am I doing something wrong? > > > > Best regards > > Galina > > PS > > >> sessionInfo() >> > > R version 2.5.1 (2007-06-27) > > i386-pc-mingw32 > > > > > [[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 > >

Hi Galina, Glazko, Galina wrote: > Dear list, > > > > I am trying to do very simple query using BiomaRt: > > library(biomaRt) > > ensembl=useMart('ensembl') > > ensembl= useDataset('hsapiens_gene_ensembl',mart=ensembl) > > .. > >> ids<-c("ENSG000000282326","ENSG000000008311","ENSG000000323881") > >> hsdef <- > getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","hgnc_s ymbo > l"),filters="ensembl_gene_id",values=ids, mart=ensembl) > >> hsdef > > NULL > > > Please let me know, am I doing something wrong? The only thing you did wrong was to input three Ensembl IDs that don't exist - try entering them individually on Ensembl's website, and you will see that you get no returned value. Best, Jim > > > > Best regards > > Galina > > PS > >> sessionInfo() > > R version 2.5.1 (2007-06-27) > > i386-pc-mingw32 > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623