Pavlidis, et al. [20] demonstrated that 10 to 15 samples (or fewer in some cases) produced reproducible results, as determined by their stability measures of order and recovery. Our study demonstrates that even large experiments benefited from filtering by fraction Present; The IFN data with 10 samples and the smoking data with 20, both had improvements in FDR after filtering (Fig. 5), with approximately a 50% improvement in FDR when using a fraction Present of 0.25 for filtering.
