Figure 3 also demonstrates that chip sets differ in the power they offer to detect associations at different frequencies. Most noticeably, when averaged over common alleles the Illumina 300 k chip set offers more power than Affymetrix 500 k. For rare alleles, the opposite is true with the Affymetrix 500 k chip having more power than the Illumina 610 k chip. This is most likely due to the way in which the Illumina SNP sets have been designed to specifically tag the common variation present in the HapMap panels.
