Filtering increased the average number of probe sets that met an FDR of 0.1 in the IFN data for experiments of all sizes (Fig. 9), and was particularly helpful for the smaller experiments: over 3-fold improvement for the 3 sample experiments (38 to 122) and nearly double for the 4 sample experiments (378 to 672). Small experiments (3–4 samples) have limited power to detect changes, and very few probe sets can be consistently identified (Fig. 8). Filtering by fraction Present greatly improves FDR even for small experiments, and retains nearly all of these reproducible probe sets (Figs. 7, 8). While we think that experiments should use more than 3 or 4 samples, this filtering method should improve results from small experiments such as pilot projects.
