For each SNP array, we selected one example with strong waves and displayed their signal intensities on chromosome 11, where the wavy patterns are especially easy to discern visually (Figure 1). Although, different samples were selected from each platform, when we compared the four arrays, we found the waves had similar periods and phases at similar genomic regions, indicating that regions with inflated or deflated signal intensities in one array are likely to show similar patterns in other arrays. However, the directionality of the magnitude of waves can be identical or opposite between arrays, that is, the waves can be either ‘in phase’ or ‘of opposite phase’ with each other: we specifically selected examples where the peaks of one Illumina (or Affymetrix) array correspond to troughs of another Illumina (or Affymetrix) array. In addition, the magnitude of waves can be different between different genotyped samples: for example, the sample in Figure 1D showed more obvious wave patterns than other genotyped samples.
