The more significant probe sets (p ≤ 0.001) were mostly retained when filtering was at ≤ 50% Present (Table 5). The FDR is similarly improved by filtering (Fig. 7; note the differences in scales in each panel for Figs. 6 and 7). Similar permutations were performed using the Smoking data for samples sizes of 6, 10 and 14. The number of probe sets with p ≤ 0.001 increased nearly 3-fold going from 6 to 10 samples; increasing to 14 sample added another 70% and the full 20 samples had a further 60% improvement over 14.
