fix: raise ValueError when combat batch has fewer than 2 cells#3994
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flying-sheep merged 3 commits intoMar 14, 2026
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Previously, `sc.pp.combat` would silently produce NaN values when a batch contained only 1 cell, because within-batch variance cannot be estimated from a single observation. This adds input validation to raise a clear error before computation begins. Closes scverse#1175
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Hi, just checking if this PR is ready for review. CI is green and tests pass. Happy to address any feedback! |
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OK, I simplified this a bit by reusing the groupby object, looks great! |
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Thanks for the simplification — reusing the groupby dict is much cleaner! |
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… fewer than 2 cells
flying-sheep
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… batch has fewer than 2 cells) (#4001) Co-authored-by: LiudengZhang <99156394+LiudengZhang@users.noreply.github.com>
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What
Raise a
ValueErrorwhensc.pp.combatreceives a batch with fewer than 2 cells.Why
ComBat estimates within-batch variance, which requires at least 2 observations.
When a batch contains only 1 cell, the variance is zero, causing a divide-by-zero
that silently fills the entire corrected matrix with NaN. Downstream functions
like
highly_variable_genesthen fail with cryptic errors.How
Added validation after batch grouping that checks all batch sizes ≥ 2. Raises a
clear error listing the offending batch names, so users know which batches to
filter before running combat.
Testing
Added
test_combat_single_cell_batch— creates a dataset with a single-cellbatch and confirms the
ValueErroris raised. All 5 existing combat testscontinue to pass.
Closes #1175