Effect of Filtering on false discovery rate (FDR). Filter method and values (x-axis): Fraction Present (FP), signal (S) or RMA value (R) followed by threshold value; separate lines are shown for each. Closed circles represent values from fraction Present filtering, open diamonds from average signal or average RMA. P-values: 0.05 (blue), 0.01 (pink), and 0.001 (green). A) IFN data, MAS5, B) IFN data, RMA, C) Smoking data, MAS5. Note that the smoking data was scaled to 100 instead of 1000 used for the other data sets.