edegR, export TMM normalized method
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Entering edit mode
6.0 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 normlized 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 approciate.

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 ?

RNA-Seq edgeR TMM CPM RPKM • 3.2k views
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1
Entering edit mode
6.0 years ago
Sam ★ 3.8k

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

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