Distribution and correlation of the LOH/CNV frequency values predicted by the HWE-based and SI-based methods. (A) For 54,001 markers, the frequencies of copy loss (SI loss) and gain (SI gain) were calculated based on signal intensities using the output from PennCNV analysis. Frequencies of copy loss (HWE loss) and gain (HWE gain) were calculated based on a generalization of the Hardy-Weinberg principle for more than two allele frequencies by considering an extra allele frequency. These frequencies are presented as an overlay plot in which the X scale represents the 54,001 markers first sorted by the SI loss values and then by chromosomal position. (B) Table describing the expected signs for correlation between the methods for predicting CNV frequency. (C) Observed correlations between these methods.