Potential error in scanpy.tl.rank_genes_groups?
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Please make sure these conditions are met
- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
- (optional) I have confirmed this bug exists on the master branch of scanpy.
What happened?
Hi,
this recent preprint https://www.biorxiv.org/content/biorxiv/early/2023/08/20/2023.07.20.549945/DC1/embed/media-1.pdf?download=true
claims that there is an issue with
https://github.com/scverse/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py#L419C1-L423C48
that reportedly leads to log-fold changes of 30 or -30 when gene expression is 0 in a cluster.
What do you think about this?
Minimal code sample
https://github.com/scverse/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py#L419C1-L423C48
Error output
No response
Versions
master
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading the referenced section of scanpy/tools/_rank_genes_groups.py and the linked preprint's claim about zero expression and log-fold changes. Reproduce the behavior with a minimal Scanpy example, since the issue provides no executable sample. Done means determining whether the reported values are erroneous and documenting the result or identifying the needed follow-up.
Written by the indexing model from the issue text.
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
- 30/100