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Question: DiffBind MA plot
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gravatar for grundelphine
6 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?

Thanks in advance for your help!

Delphine

ADD COMMENTlink modified 6 months ago by Rory Stark2.5k • written 6 months ago by grundelphine0
2
gravatar for Rory Stark
6 months ago by
Rory Stark2.5k
CRUK, Cambridge, UK
Rory Stark2.5k 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

ADD COMMENTlink written 6 months ago by Rory Stark2.5k

thanks for this quick and detailed answer!

ADD REPLYlink written 6 months ago by grundelphine0

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

ADD REPLYlink written 4 weeks ago by Vince Schulz60

I'll put it on the list!

ADD REPLYlink written 6 days ago by Rory Stark2.5k
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