edegR, export TMM normalized method

Question

[lilingjoyo]

Hello, everyone.

I'm using edgeR perorming normalization on my raw count data. The problem is that I don't know how to export normalized data. I searched lots bbs, answers shows below:

d$pseudo.alt

cpm()

rpkm()

These answers make me even more confused:

1. for d$pseudo.ald, some say it's not appropriate.
2. for cpm and rpkm. I think these are two normalized methods. Can I computed cpm or rpkm after TMM normalization? If so, it means I use two different normalization methods at same time?

Answer 1

[Sam]

It all depends on what you want to do. If you only want to get the normalized count, you can do

counts.per.m <- cpm(d, normalized.lib.sizes=TRUE)

based on answer here