edgeR default normalization method
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Homer • 0
@homer-18328
Last seen 4.8 years ago

The help page for edgeR::calcNormFactors() says

The default method was changed from "TMM" to "TMMwsp" in the Bioconductor 3.9 release.

However, I still get the results from the TMM method by default, not the TMMwsp method. Am I doing something wrong or is this a bug/error in the documentation?

edger • 1.0k views
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@gordon-smyth
Last seen 5 hours ago
WEHI, Melbourne, Australia

The documentation note is incorrect. We had been planning to change the default but, in the end, decided not to do so and the note got left behind. I will remove it.

The default methods is always the first of the methods listed in the usage line. "TMM" is first in the list so you can tell it is the default.

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