Since different DNA samples demonstrate varying magnitude of waviness, we have developed two quantitative measures to summarize the signal fluctuation patterns for genotyped samples. The first measure, called WF, summarizes the total signal fluctuation of a genotyped sample across the genome (see Methods section). The second measure, called GCWF, specifically summarizes the fraction of signal fluctuation that correlates with patterns of GC distribution. Since signal fluctuation can be caused by many factors, including genotyping array defects, presence of large CNVs, cell-line induced rearrangements and local GC content, the GCWF measure effectively measure the fraction of signal fluctuation that can be explained by genome-wide patterns of GC distribution. Both the WF and GCWF use the median absolute deviation of signal intensities, and therefore are less affected by the presence of extreme values (such as those within CNVs) than a standard deviation measure. The WF for samples in Figure 2A and Figure 2E are −0.09 and 0.05, respectively, while the GCWF for them are −0.09 and 0.04, respectively. These measures are applicable to many different types of arrays that measure signal intensities
