Hi Brad,

I recently fixed this and it should work using the devel version of biomaRt
which you can get from here:

http://www.bioconductor.org/packages/2.7/bioc/html/biomaRt.html

Using that version I get the following:

> hapmap<-useMart("HapMap_rel27")
> hapmap<-useDataset("hm27_variation_ceu",mart=hapmap)
> listFilters(hapmap)
              name                        description
1      allele_freq        Minor Allele Frequency [>=]
2           center                  Genotyping Center
3         platform                Genotyping Platform
4      monomorphic                   Monomorphic SNPs
5      marker_name                List of HapMap SNPs
6             utr3                             3' UTR
7             utr5                             5' UTR
8     coding_synon     Exons - synonymous coding SNPs
9  coding_nonsynon Exons - non-synonymous coding SNPs
10        intronic                            introns
11           chrom                         chromosome
12           start                      From position
13            stop                        To position
14       gene_list                      List of Genes
15   encode_region                      ENCODE region
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin8.11.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.5.1

loaded via a namespace (and not attached):
[1] RCurl_1.2-1 XML_2.6-0


Cheers,
Steffen


On Thu, Jun 24, 2010 at 3:40 PM, Brad McNeney <mcneney@gmail.com> wrote:

> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

