For the four genotyped samples in Figure 1, we calculated their pairwise correlation coefficients of median LRR values in 1 Mb nonoverlapping windows of autosomes (Supplementary Table 1). The absolute values of these correlations range from 0.73–0.91, further demonstrating that the locations of peaks and troughs in signal intensity are consistent across arrays. Therefore, the presence of genomic waves is unlikely to be an artifact caused by probe hybridization or data normalization specific for each particular SNP genotyping platform. It is of interest to investigate what genomic features correlate with the peaks and troughs of the waves.
