Workflow of MAnorm. MAnorm takes the coordinate of all peaks and aligned reads in both samples as input. The (M, A) value of each common peak is then calculated and plotted, where M = log2 (Read density in sample 1/Read density in sample 2) and A = 0.5 × log2 (Read density in sample 1 × Read density in sample 2). Robust regression is subsequently applied to the (M, A) values of all common peaks and a linear model is derived. Finally, the linear model is extrapolated to all peaks for normalization. A P-value is also calculated for each peak to describe the statistical significance of read intensity difference between the two samples being compared.