This is a complex question and there are perhaps no fully satisfying
approaches.  Note that the task of reannotating the affy chip is not a
concern of any Bioconductor software.  But there are resources that may
help.  Making an immense query to Biomart seems unwise but others may have
other views.

You may wish to take note of the package

SNPlocs.Hsapiens.dbSNP.20100427

available from Bioconductor.  It includes SNP metadata with provenance

"The source data files used for this package were created by NCBI on 24-26
March 2010.

WARNING: The SNPs in this package are based on the GRCh37 genome. Note that
the GRCh37
genome is the same as the hg19 genome from UCSC except for the mitochondrion
chromosome.

Therefore, the SNPs in this package can be "injected" in
BSgenome.Hsapiens.UCSC.hg19 but this
injection will exclude chrM (i.e. nothing will be injected in that
sequence).

See http://www.ncbi.nlm.nih.gov/snp, the SNP Home at NCBI, for more
information
about dbSNP.

See ?injectSNPs in the BSgenome software package for more information about
the SNP injection
mechanism.
See http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=
hg19 for more information about the Human Feb. 2009 (GRCh37/hg19) assembly
used by the
UCSC Genome Browser."

clearly noted in the Reference manual pages for the package, accessible at

http://www.bioconductor.org/packages/release/data/annotation/html/SNPlocs.Hsapiens.dbSNP.20100427.html

if you take the time to learn how to work with the SNPlocs package, you will
be able to get more current location data in various formats.  A discussion
of how to bring that information in the context of reannotating the 6.0 chip
requires much more information regarding objectives.

On Thu, May 6, 2010 at 9:51 AM, Kay Jaja <kjaja27@yahoo.com> wrote:

> Hi ,
>
> I have downloaded the Affy6.0 snp annotation file from Affy website but the
> snps are maped to an old build. for example, rs2834296 is mapped to chr 21
> and base pair position 34203263, but if you go to Ensembl you will find this
> snp has a different name rs4591 and the base pair is  35281393.
> I needed to remap all the snps to the current build so I tried biomart
> package using R using the scrip below
>
> mart <- useMart("snp")
>  mart<-useDataset("hsapiens_snp",mart)
> out=getBM(attributes=c("refsnp_id","chr_name","chrom_start"),
>  filters=c("refsnp"), values=snps, mart=mart)
>
>
> here is the problem
>
> snps is  a vector of rs# from the Affy 6.0 ( there are about 900,000) snps
> but the script took forever was never finished.
> I tried to have the vector  snps to be the only the rs# from chr 21, but
> not all the snps get mapped for example the above snps that i mentioned
> before  rs2834296 will be dropped.
>
>
> any ideas on how to map the snps in the affy 6.0  to the current build
>
> thanks and appreciate your help
>
>
>
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>
>
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