**20**wrote:

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!