Effect of filtering on average number of significant probe sets in smaller experiments. Smaller virtual experiments (4, 6 and 8 samples per treatment group) were created by random selection of arrays within each of the two treatment groups (based on 1000 permutations). The probe sets called significantly different (at the p-values shown) are shown for different values of fraction Present (x-axis). Note differences in scale for y-axes of the 3 graphs. P-values: ≤ 0.05 diamond, ≤0.01 square, ≤0.001 triangle.