Nan values after running sc.tl.filter_rank_genes_groups and plotting
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Description
Hi Team,
I'm analyzing scrna seq data from different mice tissues. I'm following the standard pipeline - preprocessing, normalizing, feature selection, clustering - currently annotating cell types(manual + reference). I've observed that when I want to study the markers cluster wise based on logfcscore, after running sc.tl.filter_rank_genes_groups and plotting - I get 'nan' values in the clusters at certain positions. Kindly assist, thank you.
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Research direction
Start by reproducing the reported pipeline around sc.tl.filter_rank_genes_groups and the subsequent plotting step, using the issue's description and image as the available context. Determine whether the NaN values originate in filtering or plotting, then define the expected cluster-wise marker output and verify the behavior with a focused regression case.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100