feat: allow exponentiation post agg for log-fold-change in rank_genes_groups

[ilan-gold]

My three questions here:

1. What to do about t-tests? Do people expect fold change of the input to the t-test (as is currently done) or fold change of the exponent?
2. How do we test this? Dummy groups? Wait for illico to compare? I added a very simple test.
3. Does the name exp_post_agg make sense? exp_post_mean?

• Closes rank_genes_groups logfoldchange different than seurat #864
• Tests included or not required because:

• Release notes not necessary because:

[codecov]

Codecov Report

❌ Patch coverage is 93.33333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.63%. Comparing base (2fa6ac0) to head (7fcdac7).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/tools/_rank_genes_groups.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4037      +/-   ##
==========================================
+ Coverage   78.60%   78.63%   +0.02%     
==========================================
  Files         118      118              
  Lines       12756    12767      +11     
==========================================
+ Hits        10027    10039      +12     
+ Misses       2729     2728       -1     

Flag	Coverage Δ
hatch-test.low-vers	77.93% <93.33%> (+0.02%)	⬆️
hatch-test.pre	78.51% <93.33%> (+0.02%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/scanpy/_settings/presets.py	86.61% <100.00%> (+0.10%)	⬆️
src/scanpy/tools/_rank_genes_groups.py	93.31% <92.85%> (+0.47%)	⬆️

[flying-sheep]

Regarding 1: I didn’t look at the math, but I assume to get both accurate logfoldchanges and correct t-test results, the t-test needs the means of the data, and the logfoldchanges need the means of e^data. So we’d have to calculate means twice I think. If @eroell doesn’t chime in I’ll re-learn the math …

Regarding 3: maybe lfc_estim_fast or so?

[ilan-gold]

Regarding 1:

I think my question is less about math than expectations. Do people expect #864 to be applied to all tests that report LFC or just wilcoxon?

Regarding 3 lfc_estim_fast

I like this but I wonder if being more explicit about the math is nicer. @eroell thoughts?

[flying-sheep]

Do people expect #864 to be applied to all tests that report LFC or just wilcoxon?

I think it would be confusing if the option only applied to one of them, but of course I don’t know what people expect.

[ilan-gold]

That's a pretty good reason! Nothing in the issue is focused on wilcoxon, I guess!

[ilan-gold]

Regarding 3: maybe lfc_estim_fast or so?

Looking back at things, I think this setting was created for a time when the code looked very different. It is only faster for t-test to do exp_post_agg.

[flying-sheep]

I think you’re right, but expm1 is a more expensive operation than the others, so doing it on the full data instead of just the means might do something. Probably not a huge factor, but let’s see.

[scverse-benchmark]

No changes in benchmarks.

Comparison: https://github.com/scverse/scanpy/compare/063262b7c2f6f7e6ca675e5efc2603e21d22df22..39712198c255e2a603c2dcfdcc8a7279f7d410e4
Last changed: Fri, 17 Apr 2026 10:43:14 +0000

More details: https://github.com/scverse/scanpy/pull/4037/checks?check_run_id=71803666404

[flying-sheep]

huh, I didn’t expect it to have zero impact. OK then, let’s see what @eroell says