after calcNormFactors with EdgeR, how to get TMM normalized matrix?
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kevin • 0
@aa1632d5
Last seen 5 weeks ago
Mexico

hi buddies!

i´m trying to normalize my count reads in Rstudio with EdgeR plugin usin the TMM method by now i just got the TMM factors, but then, what is the next step?

i ran:

pr = read.csv("feature_counts.csv", header = TRUE)

w = DEGList(pr[c(3:20]) >>>>this bcoz the rest is non numerical data

s = CalcNormFactors(w, method = "TMM")

head(s)

an object of class "DGEList" $counts... etc

and i got the following info:

$samples

  group lib.size norm.factors

s1 1 52519 0.9423

s2 1 10890 1.6654

...and so on

as i have understood, thoose are only the normalization factors, but not yet the normalized values, so whats the next step, tools, etc?

thanks

Normalization edgeR • 91 views
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@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

There concepts of "TMM normalized matrix" or "normalized values" do not exist in edgeR. If you are conducting and differential expression analysis, then there is no need for normalized counts. Have you read the edgeR User's Guide for how analyses are done?

Your question doesn't give any background or context but, if you are trying to export values from edgeR, then perhaps you are looking for cpm() or rpkm().

See

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