Hi, I Ran the following code and it did not work and asked me to report the error to the list. So here it is: ### Code#### library (biomaRt); snps <- useMart("snp", dataset="hsapiens_snp"); filters <- listFilters(snps); attributes <- listAttributes(snps); # required_attributes <- attributes[,1] required_list <- c("ENSG00000006638" ,"ENSG00000110148"); i22 <- getBM( attributes=required_attributes[30:45], filters="ensembl_gene", values=required_list, mart=snps) ### Code End ### and got the following error: >>>>>>>>>>>>> Error in getBM(attributes = required_attributes[30:45], filters = "ensembl_gene", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. >>>>>>>>>>>>> > sessionInfo() R version 2.9.0 (2009-04-17) 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_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.97-3 XML_2.3-0 -Best -Lax [[alternative HTML version deleted]]

Dear Lakshmanan thank you for posting this! I reproduced the problem, and it seems not to be trivial. We'll keep you posted via this list. Best wishes Wolfgang > Hi, > I Ran the following code and it did not work and asked me to report the > error to the list. So here it is: > ### Code#### > library (biomaRt); > snps <- useMart("snp", dataset="hsapiens_snp"); > filters <- listFilters(snps); > attributes <- listAttributes(snps); > # > required_attributes <- attributes[,1] > required_list <- c("ENSG00000006638" ,"ENSG00000110148"); > i22 <- getBM( attributes=required_attributes[30:45], > filters="ensembl_gene", values=required_list, mart=snps) > ### Code End ### > > and got the following error: > Error in getBM(attributes = required_attributes[30:45], filters = > "ensembl_gene", : > The query to the BioMart webservice returned an invalid result: the number > of columns in the result table does not equal the number of attributes in > the query. Please report this to the mailing list. > >> sessionInfo() > R version 2.9.0 (2009-04-17) > 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_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > -Best > -Lax > > [[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 -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

Hi Lakshmanan thank you for reporting this and apologies for the delayed reply. It turns out that there is a disagreement about the format of the data reported from the SNP biomart webservice that you are querying and the biomaRt R package. Resolving this seems to be a complex and slow procedure. For the time being, please do not use biomaRt with the SNP biomart, it will not work. Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber ------------------------------------------------------- > -------- Original Message -------- > Subject: [BioC] BioMart Error > Date: Fri, 4 Sep 2009 10:54:19 -0400 > From: Lakshmanan Iyer <laxvid at="" gmail.com=""> > To: Bioconductor at stat.math.ethz.ch > > Hi, > I Ran the following code and it did not work and asked me to report the > error to the list. So here it is: > ### Code#### > library (biomaRt); > snps <- useMart("snp", dataset="hsapiens_snp"); > filters <- listFilters(snps); > attributes <- listAttributes(snps); > # > required_attributes <- attributes[,1] > required_list <- c("ENSG00000006638" ,"ENSG00000110148"); > i22 <- getBM( attributes=required_attributes[30:45], > filters="ensembl_gene", values=required_list, mart=snps) > ### Code End ### > > and got the following error: >>>>>>>>>>>>>> > Error in getBM(attributes = required_attributes[30:45], filters = > "ensembl_gene", : > The query to the BioMart webservice returned an invalid result: the > number > of columns in the result table does not equal the number of attributes in > the query. Please report this to the mailing list. >>>>>>>>>>>>>> > >> sessionInfo() > R version 2.9.0 (2009-04-17) > 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_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > -Best > -Lax > > [[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 >