[BioC] getting genotypes with oligo package

[Lilia Romdhane [guest]]

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 

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

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

other attached packages:
[1] pd.genomewidesnp.6_1.10.0 RSQLite_0.11.4           
[3] DBI_0.2-7                 oligo_1.24.0             
[5] Biobase_2.20.1            oligoClasses_1.22.0      
[7] BiocGenerics_0.6.0       

loaded via a namespace (and not attached):
 [1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.2 
 [4] Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8      
 [7] ff_2.2-11             foreach_1.4.1         GenomicRanges_1.12.4 
[10] IRanges_1.18.1        iterators_1.0.6       preprocessCore_1.22.0
[13] splines_3.0.1         stats4_3.0.1          zlibbioc_1.6.0

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