What is the putative mechanism behind the GC content of probes in a microarray causing waviness?
Here is an example of "waviness" as discussed in this paper. Basically (blatently copying-and-pasting from the article): genomic waves are not platform-specific and are characterized by wavy patterns of the Log R Ratio, with identical or opposite peaks and troughs.
Log R ratio is defined as: For each SNP, let the signal intensities for the A and B alleles be denoted as X and Y, respectively. We can then calculate the R-value as Robserved = X + Y. As a normalized measure of total signal intensity, LRR is then calculated as log2(Robserved/Rexpected), where Rexpected is computed from linear interpolation of the canonical genotype clusters.