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Is sizefactors_from_controls supported by all methods?

Open grst opened this issue 3 months ago • 0 comments

Description of feature

--size_factors_from_controls and --control_features is listed under [base] in the parameter documentation, which suggests it's supported by all methods.

I'm not entirly sure, but I don't think that this is implemented for all of the methods, e.g. DREAM. Others like propd might not even support that at all (?).

The docs should make clear for which methods this is supported and parameter validation should throw an error if this is specified together with a method that doesn't support it.

Otherwise users expect that normalization worked as expected, while in reality the size factors were not calculated from the spike-in features.

grst avatar Aug 25 '25 09:08 grst