The relationship of the model selection threshold, α, with the various performance measures. This figure shows how four different performance measures vary with different values of model selection threshold, α, based on analyzing the seven simulated datasets The four performance measures are the true positive rate (TP), the true negative rate (TN), the false positive rate (FP) and the false negative rate (FN). We note that an a value between 0.02 and 0.05 generally gives a reasonable trade-off between the true positive rate and the false positive rate. a high true positive rate while maintaining a low false positive rate.
Ho et al. BMC Genomics 2009 10(Suppl 3):S16 doi:10.1186/1471-2164-10-S3-S16