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T-test / Improve simple tests #38

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merged 22 commits into from
Apr 2, 2024
Merged

T-test / Improve simple tests #38

merged 22 commits into from
Apr 2, 2024

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grst
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@grst grst commented Mar 13, 2024 •
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  • add test to ensure that pairing is working
  • throw error if there's not exactly two samples per pair
  • optimizations: use CSR for col slicing, don't copy AnnData to sort for pairing
  • Implement T-test in addition to wilcoxon test.
  • some tests still failing

Close #25

@grst grst force-pushed the improve-simple-tests branch from 37798fe to 9fb333c Compare March 13, 2024 21:22
@grst grst marked this pull request as ready for review March 14, 2024 12:57
@grst grst requested review from ilan-gold and Zethson March 14, 2024 13:10
ilan-gold
ilan-gold approved these changes Mar 18, 2024
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src/multi_condition_comparisions/methods/_simple_tests.py Show resolved Hide resolved
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grst and others added 16 commits March 18, 2024 20:48
@grst @ilan-gold
Update tests/conftest.py
607915d 
Co-authored-by: Ilan Gold <[email protected]>
@grst @ilan-gold
Update tests/conftest.py
8bebbde 
Co-authored-by: Ilan Gold <[email protected]>
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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@grst
Restructure tests
8c1e669
@grst
Fix tests for unified interface
3deeaca
@grst
Fix input checks
ff72589
@Zethson
Minor refactoring
5ce222e 
Signed-off-by: zethson <[email protected]>
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@grst
Fix numeric matrix check
4eb4c76
@grst
Pydeseq2 workaround
e8fab00
@grst
Add tests for invalid pairing detection
a4da81a
@grst
Add tests for invalid pairing detection
eacbd7f
@grst
Fix pydeseq2 test
2f45a17
@grst
Tests for wilcoxon test
f703d46
@grst
Tests for t-test
f3e5115
@grst
fix edgeR tests
0546ebf
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grst commented Apr 1, 2024

Ok, happy with this for now. I think anything else can go in a follow-up PR.
I will try to work on #36 next.

Zethson
Zethson approved these changes Apr 2, 2024
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I'd probably also vote for log2_fc instead of log_fc but it's NBD

@grst grst merged commit 7610d50 into main Apr 2, 2024
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@grst grst deleted the improve-simple-tests branch April 2, 2024 07:43
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@ilan-gold ilan-gold ilan-gold approved these changes

@Zethson Zethson Zethson approved these changes

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Support for simple wilcoxon / t-test through the same interface
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