Question: The Easiest Way To Produce The Normalised Counts In Edger
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gravatar for Nick
6.7 years ago by
Nick270
Spain
Nick270 wrote:

What is the easiest way to produce the normalised counts in edgeR? Is it just about multiplying the raw counts with the normalisation factors?

edger • 1.6k views
ADD COMMENTlink modified 6.7 years ago by Sean Davis26k • written 6.7 years ago by Nick270
1
gravatar for Sean Davis
6.7 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Check out the cpm() method in edgeR. Does that do what you want?

ADD COMMENTlink written 6.7 years ago by Sean Davis26k

I've used predFC() in the past, which produces normalized counts similar to microarray values. Not sure how different this output is from cpm().

ADD REPLYlink written 6.7 years ago by Chris Cabanski330

@Sean Davis Thanks. This seems to be the right function. I used cpm(d, normalized.lib.size=TRUE) to make use of the library normalisation.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Nick270
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