[BUG] Discrepancies between DESeq2/pyDESeq2
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Description
We are experiencing issues where specific datasets yield dramatically different results (p-values) between the R and pyDESeq2 implementations. Given that other datasets yield very similar fits and p-values, don't think this is caused by different parameters, issues with precision, etc. Happy to provide a fully reproducible example, just curious if this is a known issue or if anyone else has encountered the same issue and if there is a workaround.
Python: 3.12
pydeseq2: 0.4.3
OS: Ubuntu 22.04.3 LTS
Dataset, everything behaving as expected:
Dataset, discordant python/R results:
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Research direction
No source file or test is identified. Start by reproducing the discrepancy in the reported Python 3.12, pydeseq2 0.4.3, and Ubuntu 22.04.3 environment, using a fully reproducible dataset and comparison with the R DESeq2 results; done would require identifying and documenting the cause or a reliable workaround.
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Assessment
- Tech stack
- python, r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100