Removing only those probe sets called Absent in all samples provides the single largest improvement in FDR and appears to be sufficient for large experiments. Although the FDR is somewhat better with more stringent filtering (Fig. 7), the loss of probe sets at p ≤ 0.001 indicates there may be an accelerated loss of true positives in the larger data sets (Table 5). as the experiment size decreases, the criterion for filtering should be increased (Fig. 6, 7; Table 5). For data sets with 3–4 samples 50% Present spares most of the probe sets significant at p ≤ 0.001 and those probes sets found most consistently (Fig. 6, 8). For more samples, relaxing the threshold to 25% fraction Present is reasonable (Fig. 6, 7, and 8). Requiring 100% Present in one of the two treatment groups is not recommended, because it removes too many highly significant probe sets (Tables 2 and 5) and removes a large portion of the probe sets turned on or off (Table 4) in experiments of any size.
