Figure 6

Correlations of randomly sampled pairs of genes by percentage of Affymetrix present calls. Top: Histograms of the average number of present calls for the 5000 pairs of genes, showing three peaks at the ends and in the middle of the range. The red lines seperate the peaks and indicate the grouping of the percentages used in the bottom part of the figure. Looking at Figure 5, we identify the groups with pairs of genes where both genes are mostly absent (left peak), where both genes are mostly present (right peak), and where one gene is mostly absent and the other mostly present (central peak). Bottom: Summary curves for the correlations as a function of the product of standard deviations. The different curves correspond to the three groups of pairs of genes as identified in the histograms above. Note how correlations are consistently positive for absent/absent pairs and consistently negative for absent/present pairs in case of RMA and MBEI. Only the present/present pairs appear to be reasonably uncorrelated throughout.