In this article we described the impact of genomic waves on the quality of signal intensity data generated using several high-density SNP genotyping platforms, and investigate the underlying mechanism for their presence. Our experimental analysis illustrated the importance of DNA preparation for the Illumina Infinium platforms in achieving the best genotyping data quality, and this is likely the case for other microarray platforms, such as the Affymetrix platform. In addition, we showed that our computational approach can reduce the effects of genomic waves and salvage data for CNV analysis when wavy signal patterns are present.
