Figure 4

Number of significant probe sets after filtering. A) Filtering by fraction Present vs. by average MAS5 signal. The probe sets called significantly different (at the p-values shown) between the interferon treated and untreated samples in the 10 sample experiment are plotted against the threshold of Fraction Present (FP) or average signal (S), followed by threshold value. The horizontal line at 1230 indicates the number of probe sets at p ≤ 0.001 in the unfiltered data. Paired thresholds remove comparable numbers of probe sets, e.g. FP>0 and S254. B) Filtering by fraction Present vs. by average RMA value. (FP) Fraction Present, (R) average RMA value, followed by threshold value. The line at 1641 indicates the number of probe sets at p ≤ 0.001 in the unfiltered data.