getting genotypes with oligo package

[[email protected]]

Hi, I have genotyped samples from Affy6.0 platform using crlmm algorithm
from Oligo and I am facing difficulties in interpretation. I am trying
to match the SNP calls from crlmm with their respective alleles. I would appreciate any comments and help.
Given a SNP has A and B allele, is it that A is always a major allele
and B is always a minor allele or is it that the allele A and B are
alphabetically assigned; the first alphabet (A,T,G,C) gets assigned as
A allele and the next alphabet is assigned as B allele?
I used the code provided in the oligo package help. I would greatly obtain a result in a tabulated file like below:
NA06985.CEL NA06991.CEL
SNP_A-1507972 TT TC
SNP_A-1510136 AG GG

Thanks

[mastal]

I suspect that A would be the major allele and B the minor allele, but I don't know for sure.

Try posting your question on the Bioconductor mailing list:

http://www.bioconductor.org/help/mailing-list/

[[email protected]]

Thanks for response. I have posted this question on the Bioconductor mailing list and I 'm waiting for an answer ....