Regress_out function sets means of genes to zero
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Description
I want to use the regress_out function, analyse my data set, and then sub-cluster (for which I want to run highly_variable_genes again). However, this is not possible as the regress_out function removes the offset and therefore sets the means of genes to zero, so then the hvg function cannot be run reliably (see previous issue). I found a closed issue mentioning this problem and suggesting to ''add the offset again'. However I do not know how to do this. Could someone explain it to me?
Originally posted by @VivianeSchulz in https://github.com/scverse/scanpy/issues/707#issuecomment-1446770111
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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 regress_out and highly_variable_genes documentation or source, then review the referenced previous issue 707. Determine whether the documented behavior supports rerunning highly_variable_genes after regression and what offset restoration, if any, is expected; the issue is resolved when that behavior or guidance is clarified.
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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
- 25/100