The Easiest Way To Produce The Normalised Counts In Edger

Question

[Nick]

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

Answer 1

[Sean Davis]

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

[Chris Cabanski]

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

[Nick]

@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.