Although we have applied our method to correct genomic waves on the Illumina platforms, this method may be readily extended to other whole-genome arrays, such as array-CGH with BAC clones or whole-genome oligo–nucleotide arrays. Unlike SNP genotyping arrays, these arrays utilize hybridization of nonpolymorphic probes, however the data normalization techniques (especially the derivation of LRR) could still be applied to such data for reducing variation across markers, and then for building regression models for signal intensity adjustments. Similarly, for SNP genotyping arrays with nonpolymorphic markers, the LRR values can also be derived using the same multisample normalization approach.
