[BUG] stuck on dds.deseq2()
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- Dominant language
- Python
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- 761
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- Merged PRs (30d)
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Description
Everytime I DeseqDataSet using my own data (as counts/metadata dataframes or straight from my anndata object) or using the test data on the GettingStarted docs, I then try to run dds.deseq2() and the RAM shoots up and the kernel crashes.
The parameters for DeseqDataSet in the tutorials and the current version do not match.
Reallly would've liked to use this tool :(
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 kernel crash with the test data from the GettingStarted documentation, then compare its DeseqDataSet parameters with the current version. Investigate the dds.deseq2() execution and check whether both dataframe and anndata inputs show the same memory growth. Done means the documented examples complete without exhausting RAM or crashing the kernel.
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
- Mostly clear
- Newbie friendliness
- 35/100