edegR, export TMM normalized method
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Entering edit mode
7.0 years ago
lilingjoyo ▴ 40

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?
RPKM edgeR TMM RNA-Seq CPM • 3.5k views
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Entering edit mode
7.0 years ago
Sam ★ 4.5k

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)