Table 1.

Results of the simulation study

No normalizationQuantile normalization
IndexBlocking, randomizationTPRFPRTPRFPR
aYes, across all samples0.97 (0.02)0.002 (0.005)1 (0)0.19 (0.03)
bYes, within balanced batches0.97 (0.02)0.001 (0.003)1 (0)0.18 (0.03)
cYes, within unbalanced batches0.92 (0.04)0.10 (0.17)1 (0)0.24 (0.07)
dNo, across all samples0.95 (0.03)0.02 (0.05)1 (0)0.19 (0.04)
eNo, within balanced batches0.95 (0.03)0.01 (0.02)1 (0)0.18 (0.04)
fNo, within unbalanced batches0.92 (0.05)0.17 (0.26)1 (0)0.24 (0.07)
gYes, no0.97 (0.01)0.001 (0)1 (0)0.24 (0.02)
hNo, no0.84 (0.01)0.07 (0.03)1 (0)0.17 (0.02)
iCompletely confounded0.89 (0.08)0.20 (0.30)0.999 (0.001)0.26 (0.09)

NOTE: Mean and SD (in parenthesis) of TPR and FPR are reported. Simulation settings with the highest TPR and the lowest FPR are indicated in bold type. Simulation settings with the second highest TPR and the second lowest FPR are indicated in bold italic font.