Hi I was asked to report this error while running biomaRt. I believe it meant report to the list and/or developer! So here it goes! > i2 <- getBM( attributes[c(3:6,16,17,28,62),1], filters="ensembl_gene", values="ENSG00000090861", mart=snps) V1 1 Query ERROR: caught BioMart::Exception::Usage: Attribute dbSNP NOT FOUND Error in getBM(attributes[c(3:6, 16, 17, 28, 62), 1], filters = "ensembl_gene", : 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) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C 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_0.92-0 tools_2.8.1 XML_1.98-1 > -Best -Lax

Dear Lakshmanan thank you for reporting this! In the future, please send a fully reproducible example (I cannot tell what the values of your "attributes" and "snps" variables are). Also, can you please try downloading and installing the most recent version of biomaRt from http://www.bioconductor.org/packages/devel/bioc and then tell us whether a problem persists. (For better or worse, the online webservice that biomaRt connects to updates more frequently, and at different times, than Bioconductor releases.) Thank you Wolfgang ------------------------------------------------ Wolfgang Huber EMBL http://www.ebi.ac.uk/huber > Hi > I was asked to report this error while running biomaRt. I believe it > meant report to the list and/or developer! > So here it goes! > >> i2 <- getBM( attributes[c(3:6,16,17,28,62),1], filters="ensembl_gene", values="ENSG00000090861", mart=snps) > V1 > 1 Query ERROR: caught BioMart::Exception::Usage: Attribute dbSNP NOT FOUND > Error in getBM(attributes[c(3:6, 16, 17, 28, 62), 1], filters = > "ensembl_gene", : > 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) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > 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_0.92-0 tools_2.8.1 XML_1.98-1 > -Best > -Lax > > _______________________________________________ > 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