A plot of the true versus estimated q-values from simulations described in the text. The solid gray line shows the results averaged over 30 simulations when using a design similar to that of Choe et al. . The solid black line is the analogous comparison when using three independent individuals. The dashed line represents equality; conservatively estimated q values should fall beneath this line. The Choe et al.  design produces anti-conservative q-values estimates due to the incorrect underlying p-values, while the more statistically sound design produces conservative q-value estimates. The Monte Carlo variation of the q-value estimates is small enough that these conclusions are not affected.