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70 C. Cheng<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

Model 1<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 3<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 5<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 7<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 9<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

API Ip<br />

API Ip<br />

API Ip<br />

API Ip<br />

API Ip<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

0.0 0.2 0.4 0.6 0.8 1.0<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

1 20 40 60 100<br />

FDR control level in %<br />

BH AFDR<br />

Model 2<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 4<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 6<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 8<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Model 10<br />

1 20 40 60 100<br />

FDR control level in %<br />

q-value<br />

Fig 4. Simulation results on the rejection criteria. Each panel corresponds to a model configuration.<br />

Panels in the left column correspond to the “high noise” case σ = 3, and panels in the<br />

right column correspond to the “low noise” case σ = 1. The performance statistics �FDR (bullet)<br />

and �<br />

FNDP (diamond) are plotted against each criteria. Each panel has three sections. The left<br />

section shows FDR control with the Benjamini & Hochberg [3] adaptive procedure (BH AFDR),<br />

and the middle section shows FDR control by q-value, all at the 1%, 5%, 10%, 15%, 20%, 30%,<br />

40%, 60%, and 70% levels. The right section shows �FDR and FNDP � of API and Ip.<br />

API Ip<br />

API Ip<br />

API Ip<br />

API Ip<br />

API Ip

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