Scatter plots of intensity vs log variance and histograms of p values for all methods and data sets. A and B show simulated high variance null hypothesis data (n = 6); C and D show HGU133A data with the "spiked-in" genes removed. (A) Scatter plot of intensity versus pooled log variance (1 iteration). (B) Histograms of p values (1000 iterations). (C) Scatter plot of intensity versus log pooled variance. (D) Histograms of p values (average of all 14 comparisons). Orange columns in histograms correspond to the proportion of p values ≤ 0.05.