We explored the effect of setting different thresholds for both types of filtering on the percentage of probe sets retained that have each detection call (A, P, M). When adjusted to remove comparable numbers of probe sets, filtering by fraction Present does better at retaining probe sets called Present. About 37% of the probe sets are Absent on all 20 arrays, and are therefore removed by the fraction Present filter set to any fraction greater than 0 (Fig. 3A). No Present probe sets were removed until the threshold was at least 20%, by which point 81% of the Absent probe sets were removed. Setting the fraction Present to 50% removes 4.2% of the Present probe sets along with 92% of the Absent probe sets (Fig. 1B and 3A). Filtering by either signal value (Fig. 3B) or RMA value (Fig. 3C), when adjusted to remove a comparable number of probe sets, leaves a less favorable balance between Absent and Present probe sets. Unlike filtering by fraction Present, signal-based filtering removes Present probe sets even when using a very low minimum MAS5
