biomaRt and wormbase: gene dataset
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@giovanni-coppola-893
Last seen 10.2 years ago
Hello, I am trying to get human and mouse homologs from worm genes. I am querying wormbase using biomaRt. I get an error when trying to use the 'gene' dataset (example below). The other datasets work fine. Is there a way around this? Thanks Giovanni library(biomaRt) Loading required package: XML Loading required package: RCurl mart<-useMart("wormbase") listDatasets(mart) dataset version 1 goterm 2 variation 3 expr_pattern 4 phenotype 5 gene 6 paper 7 rnai mart <- useDataset(dataset = "gene", mart = mart) Entity: line 1: parser error : Start tag expected, '<' not found Dataset name conflict for gene. Need to further qualify with the virtualSchemaNa ^ Error in .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), : error in creating parser for Dataset name conflict for gene. Need to further qualify with the virtualSchemaName as well > sessionInfo() R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt RCurl XML "1.6.0" "0.6-0" "0.99-6"
biomaRt biomaRt • 1.0k views
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