what does lowess smoothed line show in a MA plot

Question

[Zhilong Jia]

What exactly does lowess smoothed line show in a MAplot figure?

Since lowess means kind of local regression, it seems that lowess smoothed line shows the bias of regulated genes to up or down in different expression levels. Am I wrong? Or any other explanation? An example figure will be better.

Thank you

Answer 1

[JC]

The line visually indicates how much bias do you have for up or down regulated genes with a fixed threshold (such as M=1 or M=-1), because you expect this line to be horizontal at M=0.

[Zhilong Jia]

How to set this kind of threshold? Like a R code: lines(lowess(MAobj$M~MAobj$A))? Ref: https://support.bioconductor.org/p/33197/ Thank you.