The Log R Ratio (LRR) value is originally developed on the Illumina platform as a normalized signal intensity measure (11). For each SNP, let the signal intensities for the A and B alleles be denoted as X and Y, respectively. We can then calculate the R-value as Robserved = X + Y. As a normalized measure of total signal intensity, LRR is then calculated as log2(Robserved/Rexpected), where Rexpected is computed from linear interpolation of the canonical genotype clusters (11). For the Illumina SNP arrays, the LRR values can be directly calculated and exported from the BeadStudio software. For the Affymetrix platform, we first extract allele-specific signal intensity values (X and Y) by the Affymetrix Power Tools (http://www.affymetrix.com/support/developer/powertools/index.affx), then construct the canonical genotype clusters using all genotyped samples and calculate the LRR values. The Affymetrix genome-wide 6.0 and the Illumina HumanHap1M arrays contain nonpolymorphic markers to improve genome coverage. For each nonpolymorphic marker in each sample, we take the median value of all samples as the Rexpected value for computing the LRR values.
