Hi I was carrying out the following biomaRt query: getBM(attributes=c("ensembl_gene_id","hgnc_symbol","description"), filter="ensembl_gene_id", value=ids, mart=mart) and I got the following error: 1 Query ERROR: caught BioMart::Exception::Database: Error during query execution: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'AND main.gene_id_1020_key=ensembl_mart_51.hsapiens_gene_ensembl_ Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "description"), : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. I don't get errors with queries made to the ENSEMBL 51 VARIATION database but get them when using the ENSEMBL 51 GENES database sessionInfo() R version 2.6.1 (2007-11-26) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY =en_GB;LC_MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_GB;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.14.1 RCurl_0.8-3 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 XML_1.93-2 -- Sonia Shah Bloomsbury Centre for Bioinformatics Department of Computer Science New Engineering Building Malet Place London WC1E 6BT

Hi Sonia. I don't know what you have in your 'ids' variable, but this command works fine for me on the latest version of R/biomaRt. I suspect updating your version of R/biomaRt is all you need ... see below for my commands on a fresh R session. Also, I think there have been a couple minor internal biomart changes in that time. Cheers, Mark ------------ > library(biomaRt) > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > getBM(attributes=c("ensembl_gene_id","hgnc_symbol","description"), filter="ensembl_gene_id", value="ENSG00000060237", mart=mart) ensembl_gene_id hgnc_symbol 1 ENSG00000060237 WNK1 description 1 Serine/threonine-protein kinase WNK1 (EC 2.7.11.1) (Protein kinase with no lysine 1) (Protein kinase, lysine-deficient 1) (Kinase deficient protein) (Erythrocyte 65 kDa protein) (p65) [Source:UniProtKB/Swiss-Prot;Acc:Q9H4A3] > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 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_0.91-0 XML_1.98-1 ------------ On 21/11/2008, at 9:51 PM, Sonia SHAH wrote: > Hi > > I was carrying out the following biomaRt query: > getBM(attributes=c("ensembl_gene_id","hgnc_symbol","description"), > filter="ensembl_gene_id", value=ids, mart=mart) > > and I got the following error: > 1 Query ERROR: caught BioMart::Exception::Database: Error during > query execution: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL server version for the right > syntax to use near 'AND > main.gene_id_1020_key=ensembl_mart_51.hsapiens_gene_ensembl_ > Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", > "description"), : > Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please > report. > > I don't get errors with queries made to the ENSEMBL 51 VARIATION > database but get them when using the ENSEMBL 51 GENES database > > sessionInfo() > R version 2.6.1 (2007-11-26) > x86_64-unknown-linux-gnu > locale: > LC_CTYPE > = > en_GB > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_GB > ;LC_COLLATE > = > en_GB > ;LC_MONETARY > = > en_GB > ;LC_MESSAGES > = > en_GB > ;LC_PAPER > = > en_GB > ;LC_NAME > = > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB;LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] biomaRt_1.14.1 RCurl_0.8-3 > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 XML_1.93-2 > > > > > -- > Sonia Shah > Bloomsbury Centre for Bioinformatics > Department of Computer Science > New Engineering Building > Malet Place > London WC1E 6BT > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852