To examine whether wavy patterns of signal intensities exist in different types of SNP genotyping platforms, we analyzed the intensity data for the Affymetrix Mapping 500K array, Affymetrix genome-wide 6.0 array, and the Illumina HumanHap550 and HumanHap1M arrays (see Methods section). We examined the LRR value, which is a normalized signal intensity measure originally developed for the Illumina platform (11), but we note that it can be adapted to the Affymetrix platform as well (see Methods section). The LRR value for a probe is a measure of the difference between the signal intensity of the test sample and a pool of reference samples of the same SNP genotype. This measure is a preferred signal intensity summarization measure for CNV detection, since it greatly reduces the signal variability between different markers.
