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Giovanni Coppola
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250
@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"