25% Present, MAS5 signal ≥ 375, or RMA value ≥ 4.75 leads to little improvement in FDR for the more significant probe sets (p ≤ 0.001), while increasing the number of those very significant probe sets lost (Table 2). Results for the smaller vitamin A data seta are similar (Table 2). The smoking dataset (20 arrays per group) has higher variability within each group. In those data, the fraction Present filter shows a larger advantage over the average signal filter, which increases with increasing stringency (Fig. 5C).
