Fig. 2

Box-whisker diagrams of the average absolute-value difference between the genotype-based and intensity-based AF estimates. Panels from left to right represent the results of the Affymetrix 100 K (n = 367), 500 K (n = 448), Array 6.0 (n = 1,013), and Axiom (n = 1,666) arrays, where n is the sample size. In each panel, the box-whisker diagrams on the left- and right-hand sides summarize the results of the AF estimates without the CPA + LIM adjustment (“Unadjusted”) and AF estimates with the CPA + LIM adjustment (“Adjusted”), respectively. Each box-whisker diagram summarizes the distribution of the average absolute-value difference between the genotype- and intensity-based AF estimates of whole-genome SNPs. The extreme values outside the maximum plus a 1.5 interquartile range or the minimum minus a 1.5 interquartile range are indicated by circles