[BioC] biomaRt and wormbase: gene dataset

Giovanni Coppola gcoppola at ucla.edu
Wed May 17 16:39:10 CEST 2006


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"



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