Figure 2.

Boxplots of average pairwise correlations of s between two array sets. They are stratified by average lower presence proportion in two array sets (the presence proportion of a probe set is the proportion of arrays in an array set where the target gene is called 'present' by GeneChip's algorithm). The average is taken over C(6, 2) = 15 pairwise comparison of two array sets for each probe set, and the correlation is calculated using probes that are not identified as an outlier in both array sets. The range of the average lower presence proportion for the six boxplots are: (0, 0.17), (0.17, 0.34), (0.34, 0.51), (0.51, 0.68), (0.68, 0.85), (0.85, 1). The title of each boxplot is the number of probe sets classified into this boxplot. Eleven probe sets with too few non-outlier probes to calculate correlations for all 15 comparisons are not included in the boxplots. The average lower presence proportion and average pairwise correlation for probe sets in Figure 1 are (a) 1, 0.95; (b), 0.93, 0.94; and (c) 0, 0.86.