How does edgeR normalize sequencing depth

Question

[hxlei613]

Hi everybody!

I just started to use edgeR.And I am curious about the normalization methods used to normalize sequencing depth. But I can't find exact methods in edgeR UsersGuide. It only mentions TMM method that can adjust RNA composition.

Is there someone to help me?

Thank you very much!

Answer 1

[Sean Davis]

TMM is described here.

Yes, it deals with sequencing depth in a robust way.

[hxlei613]

I have read this already. But I want to figure out the methods used to normalize sequencing depth in edgeR. Thank you any way :)

[Sean Davis]

TMM is the method used to normalize for sequencing depth. In fact, it works better than simply correcting by library size (see Figure 2 in the paper).