per treatment group (Fig. 8). The number identified as "true positives" (i.e. matching the full 10 sample experiment) at p ≤ 0.05 increases with the size of the experiment. Filtering at 50% Present removes about 50% of the false positive probe sets across the full range of sizes, and removes from 11.6% (3 samples) to 18.4% (8 samples) of the true positive probe sets (primarily those with p > 0.01). This suggests that larger experiments do not need as stringent a fraction Present filter.
