fix: run t-test on log values regardless of mean_in_log_space - #4337
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September 2, 2026 22:54
rank_genes_groups(method='t-test' | 't-test_overestim_var', mean_in_log_space=False) computed the per-group means and variances on expm1(X) and fed them to Welch's test, so the test ran on linear-scale values while the docstring and release note describe mean_in_log_space as a fold-change option only. Compute the test statistics on X, then (if requested) the exponentiated means for the fold change, as the wilcoxon branch already does. Adds a test asserting scores and p-values are identical for both settings.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #4337 +/- ##
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Coverage 81.98% 81.98%
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Files 134 134
Lines 13235 13237 +2
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+ Hits 10851 10853 +2
Misses 2384 2384
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rank_genes_groups(method="t-test", mean_in_log_space=False)runs the t-test on exponentiated values #4336test_mean_in_log_space_does_not_change_ttestassertsscoresandpvalsare identical formean_in_log_space=True/Falsewith both t-test methods onpbmc68k_reduced; it fails onmainand passes with the fix.tests/test_rank_genes_groups.pypasses.docs/release-notes/+ttest-log-space.fix.mdincluded; will rename to this PR's number)On
main(and the 1.13 pre-releases; 1.12.4 is unaffected),compute_statisticscomputed the per-group means and variances onexpm1(X)for the t-test methods whenevermean_in_log_space=False, so Welch's test ran on linear-scale values.mean_in_log_spaceis documented as a fold-change option only (#4037 release note), and the function expects log data. This computes the test statistics onX, materializes the test results, and only then recomputes the means onexpm1(X)forlogfoldchangeswhen requested, the same order thewilcoxonbranch uses.logfoldchangesare unchanged (the existingtest_mean_in_log_spacestill passes).Generated by Claude Code