CNV calling on Perlegen used a similar algorithm to the Illumina arrays but had additional preprocessing. To perform data normalization and signal extraction from the raw final report files generated in the genotyping experiments, we first reformatted data from dbGaP into the format produced by the following Affymetrix Power Tools: birdseed.calls.txt, birdseed.confidences.txt and quant-norm.pm-only.med-polish.expr.summary.txt (Supplementary Table 11). We calculated the log10 of the X and Y values provided in the sample-based report files. For each SNP marker, the allele-specific intensity for the AA, AB and BB genotypes on all genotyped samples was used to construct three canonical genotype clusters in the polar coordinates θ and R. Once canonical genotype clusters were constructed, signal intensity values for each SNP were transformed into LRR and BAF values. For details, see URLs.
