> [Bug] `rank_genes_groups` after `normalize_pearson_residuals`
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Area – Differential Expression
- Dominant language
- Python
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Description
Hi, @jlause
There's a issue when using normalize_pearson_residuals, it seems that we can't calculated the log2foldchange in rank_genes_groups will be failed. That's because np.expm1 can't restore the adata.X after normalize_pearson_residuals. Could you solve this issue that completed the downstream currently?
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Research direction
Start by reproducing the failure with normalize_pearson_residuals followed by rank_genes_groups, then read both entry points to trace how log2foldchange is calculated. Done means this downstream sequence completes successfully and produces log2foldchange values after Pearson residual normalization.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100