Dear BioC and Steffen I'd be grateful for your help. I getting an xmlTreeParse error with useDataset() Thanks Aedin > 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(dataset="hsapiens_gene_ensembl", mart=mart) Reading database configuration of: hsapiens_gene_ensembl Entity: line 1: parser error : Start tag expected, '<' not found NA ^ Error in .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), : error in creating parser for NA > traceback() 3: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), as.logical(replaceEntities), as.logical(asText), as.logical(trim), as.logical(validate), as.logical(getDTD), as.logical(isURL), as.logical(addAttributeNamespaces), as.logical(useInternalNodes), FALSE, as.logical(isSchema)) 2: xmlTreeParse(res[1, ]) 1: useDataset(dataset = "hsapiens_gene_ensembl", mart = mart) > sessionInfo() R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt XML RMySQL DBI "1.4.0" "0.99-6" "0.5-7" "0.1-10"

Hi Aedin, You should upgrade biomaRt and use the latest version (1.5.10, see developmental packages). Best, Steffen > Dear BioC and Steffen > I'd be grateful for your help. I getting an xmlTreeParse error with > useDataset() > Thanks > Aedin > > > 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(dataset="hsapiens_gene_ensembl", mart=mart) > Reading database configuration of: hsapiens_gene_ensembl > Entity: line 1: parser error : Start tag expected, '<' not found > NA > ^ > Error in .Call("RS_XML_ParseTree", as.character(file), handlers, > as.logical(ignoreBlanks), : > error in creating parser for NA > > > traceback() > 3: .Call("RS_XML_ParseTree", as.character(file), handlers, > as.logical(ignoreBlanks), > as.logical(replaceEntities), as.logical(asText), as.logical(trim), > as.logical(validate), as.logical(getDTD), as.logical(isURL), > as.logical(addAttributeNamespaces), as.logical(useInternalNodes), > FALSE, as.logical(isSchema)) > 2: xmlTreeParse(res[1, ]) > 1: useDataset(dataset = "hsapiens_gene_ensembl", mart = mart) > > > sessionInfo() > R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "base" > > other attached packages: > biomaRt XML RMySQL DBI > "1.4.0" "0.99-6" "0.5-7" "0.1-10" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >