Fig. 3
True negative rate for BAMBOO and MOD using 10 bridging controls. The effect size between the two groups after batch correction are on the x-axis and the effect size in the “true” data (i.e. before batch introduction on the simulated data) are on the y-axis. Columns show the number of outliers in the simulations and the rows the strength of the plate-wide effect. False positives (proteins that were not significantly different in the true data and found statistically significant after batch effects correction) are in red and true negatives (proteins that were not significantly different in the true data and still not statistically significant after batch effects correction) are in grey.
