Dear list, I'm attempting to use the biomaRt library to annotate a microarray data set, and get the following error message (refer below). This code (replacing 'ensembl_mart_37' with 'ensembl_mart_36') worked fine a week ago, so perhaps the latest ENSEMBL release (16/2/6) is causing biomaRt some trouble? Many thanks, Matt Ritchie > library(biomaRt) Loading required package: RMySQL Loading required package: DBI Loading required package: XML > listMarts() [1] "ensembl_mart_37" "vega_mart_37" "snp_mart_37" "msd_mart_4" [5] "uniprot_mart_17" > mart<-useMart("ensembl_mart_37") connected to: ensembl_mart_37 > listDatasets(mart) dataset version 1 mmusculus_gene_ensembl NCBIM34 2 tnigroviridis_gene_ensembl TETRAODON7 3 frubripes_gene_ensembl FUGU4 4 dmelanogaster_gene_ensembl BDGP4 5 ggallus_gene_ensembl WASHUC1 6 scerevisiae_gene_ensembl SGD1 7 agambiae_gene_ensembl AgamP3 8 mdomestica_gene_ensembl BROADO2 9 rnorvegicus_gene_ensembl RGSC3.4 10 amellifera_gene_ensembl AMEL2.0 11 btaurus_gene_ensembl Btau_2.0 12 cintestinalis_gene_ensembl JGI2 13 celegans_gene_ensembl CEL150 14 hsapiens_gene_ensembl NCBI35 15 xtropicalis_gene_ensembl JGI4 16 cfamiliaris_gene_ensembl BROADD1 17 mmulatta_gene_ensembl MMUL_0_1 18 ptroglodytes_gene_ensembl CHIMP1A 19 drerio_gene_ensembl ZFISH5 > mart<-useDataset('mmusculus_gene_ensembl', mart=mart) Reading database configuration of: mmusculus_gene_ensembl Entity: line 1: parser error : Start tag expected, '<' not found NA ^ Error in xmlTreeParse(res[1, ]) : error in creating parser for NA > sessionInfo() R version 2.2.0, 2005-10-06, i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt XML RMySQL DBI fortunes "1.5.2" "0.97-8" "0.5-5" "0.1-9" "1.2-0"

Hi Matt, This is due to an unexpected change in the Ensembl BioMart database and I have fixed that in the BioMart version available from the devel repository. Note however that we are trying to remove the dependency on RMySQL and currently are updating the biomaRt package to do queries over HTTP (will be the default) in addition to the use of MySQL. Some functions are not yet updated and might give some errors for the next few days. The functions you are trying to use should already work properly. best, Steffen > Dear list, > > I'm attempting to use the biomaRt library to annotate a microarray data > set, and get the following error message (refer below). This code > (replacing 'ensembl_mart_37' with 'ensembl_mart_36') worked fine a week > ago, so perhaps the latest ENSEMBL release (16/2/6) is causing biomaRt > some trouble? > > Many thanks, > > Matt Ritchie > > > library(biomaRt) > Loading required package: RMySQL > Loading required package: DBI > Loading required package: XML > > listMarts() > [1] "ensembl_mart_37" "vega_mart_37" "snp_mart_37" "msd_mart_4" > [5] "uniprot_mart_17" > > mart<-useMart("ensembl_mart_37") > connected to: ensembl_mart_37 > > listDatasets(mart) > dataset version > 1 mmusculus_gene_ensembl NCBIM34 > 2 tnigroviridis_gene_ensembl TETRAODON7 > 3 frubripes_gene_ensembl FUGU4 > 4 dmelanogaster_gene_ensembl BDGP4 > 5 ggallus_gene_ensembl WASHUC1 > 6 scerevisiae_gene_ensembl SGD1 > 7 agambiae_gene_ensembl AgamP3 > 8 mdomestica_gene_ensembl BROADO2 > 9 rnorvegicus_gene_ensembl RGSC3.4 > 10 amellifera_gene_ensembl AMEL2.0 > 11 btaurus_gene_ensembl Btau_2.0 > 12 cintestinalis_gene_ensembl JGI2 > 13 celegans_gene_ensembl CEL150 > 14 hsapiens_gene_ensembl NCBI35 > 15 xtropicalis_gene_ensembl JGI4 > 16 cfamiliaris_gene_ensembl BROADD1 > 17 mmulatta_gene_ensembl MMUL_0_1 > 18 ptroglodytes_gene_ensembl CHIMP1A > 19 drerio_gene_ensembl ZFISH5 > > mart<-useDataset('mmusculus_gene_ensembl', mart=mart) > Reading database configuration of: mmusculus_gene_ensembl > Entity: line 1: parser error : Start tag expected, '<' not found > NA > ^ > Error in xmlTreeParse(res[1, ]) : error in creating parser for NA > > sessionInfo() > R version 2.2.0, 2005-10-06, i686-pc-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "base" > > other attached packages: > biomaRt XML RMySQL DBI fortunes > "1.5.2" "0.97-8" "0.5-5" "0.1-9" "1.2-0" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >