hanging when finding genewise dispersions
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- Dominant language
- Python
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Description
Hello pydeseq2 devs.
Thank you all for developing this easy-to-use analysis tool. I'm running into extremely long runtimes (or possibly just hanging) when running dds.fit_genewise_dispersions(). I've seen some chatter about similar issues in the past when running dds.deseq2().
As others have pointed out, this issue appears linked to occurences of 0 within the matrix. Adding 1 to all counts seems to resolve the issue, but I'd prefer to avoid this if possible.
Does anyone have practical advice for working around this issue?
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 reproducing the long runtime in dds.fit_genewise_dispersions() with a count matrix containing zero values, and compare it with the reported workaround of adding 1 to all counts. Trace the fitting path from that entry point; done means the method completes without requiring that workaround, with behavior covered for matrices containing zeros.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100