for 3–4 samples at 50% Present and 1–2% for 5–6 samples per group at 25% Present. Only 2 probe sets in the 3-sample permutations were found to be significant at p ≤ 0.001 at least 50% of time, whereas 65 such probe sets were found in the 4-sample permutations. All of these were retained by fraction Present filtering at all thresholds.
