I have a small question about the interpretation of the colours assigned to the dots in the MA plots obtained with the DiffBind package:
red dots represent significantly differentially bound sites but what about the dark blue dots, the ones that are close to the borders and sometimes near to the red dots?
By default the MA plot is plotted using the smoothScatter function. Instead of every point being plotted, the densities of points at different regions of the plot are indicated using shades of blue. The solid blue dots are an artefact of this smoothing (DiffBind plots the red points over the smoothed plot). So solid blue points are not indicating anything meaningful.
You can see the plot without the smoothing by setting bSmooth=FALSE.