Filtering by fraction Present does a better job of removing most of the Absent probe sets while retaining most of the Present probe sets than filtering by either average MAS5 signal or RMA value (Figs. 1, 2 and 3), and results in much better FDR (Fig. 5, 7). Our main evaluation criteria, improvement of FDR, was chosen because this experiment-wide measure of confidence is widely applied. Because there is no "gold standard" for real experiments, we used measures that increased the likelihood of a result being a true positive, such as p-value < 0.001 for a Welch's t-test and consistency of detecting the difference in multiple permutations. Fraction Present filtering removes very few probe sets with p ≤ 0.001 (Fig. 4 and 6, Tables 2 and 5); it does not remove probe sets that are turned on or off unless the threshold is set above 50% Present (Table 4). Unlike using signal or RMA values, thresholds chosen for fraction Present are not affected by chip type, percent called present, method of scaling or normalization, nor by the method used to produce the expression value (e.g. MAS5, RMA).
