To investigate whether our wave adjustment procedure works on other types of arrays, we examined the GCWF values for 270 HapMap samples genotyped by the Affymetrix genome-wide 6.0 arrays. Before adjustment, the 5th and 95th percentile of GCWF values were −0.011 and 0.010, respectively. These HapMap samples do not show strong wavy patterns, since their signal intensities were normalized against a reference clustering file constructed from themselves. Nevertheless, after adjustment, these measures narrowed to −0.0046 and 0.005, respectively. Therefore, the wave adjustment procedure can be applied to different technical platforms.
