docs(pp.scale): document that variance/std use ddof=1 (sample correction)#4196
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docs(pp.scale): document that variance/std use ddof=1 (sample correction)#4196AxelMcKenna wants to merge 1 commit into
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sc.pp.scalecomputes gene-wise variance and standard deviation with Bessel's correction (ddof=1), viamean_var(x, axis=0, correction=1)inscale_arrayandscale_array_masked. This convention isn't stated anywhere in the docstring, so a reimplementation usingnumpy.std()defaults (ddof=0, population variance) silently diverges fromsc.pp.scale's output - negligible for largen_obs, but non-negligible for small datasets (e.g. ~0.02% on a ~2700-cell PBMC3k-sized dataset, enough to shift wheremax_valueclipping takes effect).This PR adds a
.. note::to thescaledocstring stating the correction used. No behavior change.