I have been reading the usersguide of limma package in order to get some useful indications about how can I define the Amean's cutoff but after following the indications provided there I got a little bit confused.
In fact, in the page 34 of the usersguide it is written: " A histogram of the Amean values and a sigma vs Amean plot may help identify a cutoff below which Amean values can be filtered"
But my problem lies in the plots, I can't figure out actually how I can define an appropriate cutoff for the Amean because they get me confused.
So far the only way I use to define my Amean cutoff is through: mean(fit$Amean).
Is that true ?
Thanks in advance !