[BioC] biomaRt: error using dataset from HapMap_rel27 mart

Brad McNeney mcneney at gmail.com
Fri Jun 25 00:40:02 CEST 2010


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.


Brad McNeney
Statistics and Actuarial Science
Simon Fraser University

> sessionInfo()
R version 2.11.1 (2010-05-31)

[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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