Figure 4

Simulation analysis for site occupancy estimation and detection of differential site occupancy. A scenario of three forms with occupancy of 5%, 20% and 75% for each is considered, where mean and standard deviation of log2-intensity are set to 25 and 0.2, respectively. The results by the naïve and proposed methods are compared based on 1000 simulations. (a) Relative errors of site occupancy estimates (i.e., estimation error divided by the true value), with different number of replicates and presence of missing data. (b) Widths of the 95% confidence intervals. (c) Type I error rate based on a statistical significance level set at 0.05. The horizontal dashed lines indicate the theoretical Type I error. The dots indicate the actual Type I error across 1000 simulations. (d) Statistical power to detect differential site occupancies with differences of 5%, 10% and 15%.