Question: DiffBind MA plot
0
12 months ago by
grundelphine0 wrote:

Hi,

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?

Delphine

maplot diffbind • 271 views
modified 12 months ago by Rory Stark2.7k • written 12 months ago by grundelphine0
2
12 months ago by
Rory Stark2.7k
CRUK, Cambridge, UK
Rory Stark2.7k wrote:

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.

Cheers-

Rory

thanks for this quick and detailed answer!

The solid blue dots can be removed by adding smoothScatter parameter nrpoints = 0 like

dba.plotMA(chipdata, nrpoints = 0)

It may be good to make that the default parameter for dba.plotMA.

Vince