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davismcc / archive-scater

An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
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minor comment for the documentation of normalize() #107

Closed friedue closed 6 years ago

friedue commented 7 years ago

The function normalize.SCESet() has the default parameter recompute_cpm = TRUE - the current help text does not mention that the additional prerequisites for this parameter are (i) the presence of actual values within cpm(sceSet) and (ii) exprs_values must be set to “counts”.

Since the default of the function that creates an sceSet object is to store cpm values in the exprs() slot, I was puzzled why normalize() would not re-compute the cpm values because I wasn't aware that they needed to be actually stored in the dedicated cpm() slot.

davismcc commented 6 years ago

This issue was moved to davismcc/scater#20