The distribution of RMA values (Fig. 2A) has a greater abundance of probe sets with low values than does the MAS5 signal, and more of the probe sets called Present have low values (compare Figs. 1A and 2A). Filtering by a threshold of 50% Present leaves many of the low-level Present probe sets (Fig. 2B). In contrast, filtering by the average RMA value ≤5.03, which removes a comparable number of probe sets, removes the low probe sets and truncates the left-most portion of the graph (Fig. 2C).
