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The Easiest Way To Produce The Normalised Counts In Edger

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
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updated by Sean Davis Sean Davis • written by Nick Nick

1 answer

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

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written by Sean Davis Sean Davis

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

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written by Chris Cabanski • Chris Cabanski

@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.

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written by Nick Nick

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