I am trying to extract certain information from Axiom and Axiom Exome arrays from Affymetrix. I have done the same for GenomeWildSNP 6 using oligo, crlmm and others though R but those packages does not support Axiom and Axiom Exome technologies (or I have not been able to use them).

So actually I'm using Affymetrix Power Tools (APT 1.15.1) user linux to extract the genotype (apt-probeset-genotype) and to extract the intensities to perform the BAf and the L2R calculations (pat-probeset-summarize):

apt-probeset-summarize --cdf-file /DATA/Axiom_Exome_analysis.r2/Axiom_Exome_1A.r2.cdf 
    --analysis quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true 
    --target-sketch /DATA/Axiom_Exome_analysis.r2/Axiom_Exome_1A.r2.AxiomGT1.sketch 
    --out-dir /DATA/expression 
    --cel-files /DATA/ListCelAxiomExome.txt

With the output of apt-probeset-summarize I calculate BAF and L2R:

thita = arctan( Yij / Xij ) / ( pi / 2 ) | Xij, Yij: Intensities for A-Allele and B-Allele
BAFi =  0                                        , thita < 0.1
        ( 0.5 * ( thita - 0.1 ) ) / 0.4          , 0.1 <= thita < 0.5
        0.5 + ( ( 0.5 * ( thita - 0.5 ) ) / 0.4 ), 0.5 <= thita < 0.9
        1                                        , thita >= 0.9
L2Ri = log2( xij / median( xi )

And then I relate the BAF and the L2R with the genotype:

apt-probeset-genotype --analysis-files-path /DATA/Axiom_Exome_analysis.r2 
    --xml-file /DATA/Axiom_Exome_analysis.r2/Axiom_Exome_1A_96orMore_Step1.r2.apt-probeset-genotype.AxiomGT1.xml 
    --out-dir /DATA/genotype 
    --cel-files /DATA/ListCelAxiomExome.txt

But I'm misunderstanding something or using in a bad way the tools because if we check the genotype and the BAF:

> head( res );
             L2R.X219    L2R.X220   L2R.X221 B.X129 B.X220 B.X221
AX-11092599  0.8267903  1.0000000  1.0039047    0.5    0.5    0.5
AX-11092615  1.0000000  0.9951315  1.0152408    0.5    0.5    0.5
AX-11092926  1.1046545  1.0000000  0.8545519    0.5    0.5    0.5
AX-11094576  0.9953893  1.0000000  1.0047053    0.5    0.5    0.5
AX-11095131  0.9954416  1.0000000  1.0012461    0.5    0.5    0.5
AX-11096558  1.0124673  0.9890515  1.0000000    0.5    0.5    0.5

> head( calls )
            probeset_id G.X219L G.X220 G.X221
AX-11092599 AX-11092599      AA     AB     AB
AX-11092615 AX-11092615      AA     AA     AA
AX-11092926 AX-11092926      BB     AB     AA
AX-11094576 AX-11094576      AA     AA     AA
AX-11095131 AX-11095131      AA     AA     AA
AX-11096558 AX-11096558      BB     BB     BB

The summary is a little bit better:

> summary( res$B.X129 )
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 0.2545  0.5000  0.5000  0.5005  0.5000  0.8624

But when I plot the BAF I expect to see 3 ranges: AA at the bottom, AB in the middle and BB at the top. But this is the result:

So... Can someone help me to extract properly the intensities and calculate BAF/L2R in a right way?

Thanks in advance!