[BioC] biomaRt: error using dataset from HapMap_rel27 mart
Brad McNeney
mcneney at gmail.com
Fri Jun 25 00:40:02 CEST 2010
Hello,
I'm trying to use biomaRt to access SNP data from HapMap_rel27.
> library(biomaRt)
> hapmap<-useMart("HapMap_rel27")
gives no trouble and I can list the available datasets. When I try to
use any of the datasets I get the following:
> hapmap<-useDataset("hm27_variation_ceu",mart=hapmap)
Checking attributes ...Error in bmAttrFilt("attributes", mart) :
biomaRt error: looks like we're connecting to incompatible version
of BioMart suite.
Can anyone suggest a work-around or error in what I'm doing? Or is it
just not possible to access HapMap_rel27 with biomaRt?
Session information included at the end of this message.
Thanks,
Brad
---
Brad McNeney
Statistics and Actuarial Science
Simon Fraser University
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.4.0
loaded via a namespace (and not attached):
[1] RCurl_1.4-2 tools_2.11.1 XML_3.1-0
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