biomaRt and wormbase: gene dataset
0
0
Entering edit mode
@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
ADD COMMENT

Login before adding your answer.

Traffic: 552 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6