search

tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
86 stars 8 forks source link

_collect_metacell() performs unweighted geomean for regularization values #59

Closed orenmn closed 11 months ago

orenmn commented 11 months ago

in metacells/pipeline/collect.py, _collect_metacell() performs a weighted geomean for the regularized expression (by the way, why not use scipy.stats.mstats.gmean with the weights parameter?), yet performs an unweighted geomean for the regularization values, i.e., current code does: regularization_of_metacell = ss.mstats.gmean(regularization_per_cell_of_metacell) while seems to me the code should be: regularization_of_metacell = ss.mstats.gmean(regularization_per_cell_of_metacell, weights=weight_per_cell_of_metacell)

orenbenkiki commented 11 months ago

Should be fixed by commit cea46935f8a29661e0761e8cbbd7fb0afdfa7590 - will be eventually published in 0.9.4.