Stuck at Fitting MAP dispersions... ... done in 0.54 seconds.
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Description
When doing DEG analysis, I declined the number of tested cell from 20,000 to 4000, the dds.fit_LFC() wont start:
🔬 分析 TAK-901 vs Control (整体数据)
🔬 开始分析: TAK-901 vs DMSO_TF
分析名称: Overall_TAK-901_vs_Control
原始样本数 - TAK-901: 271, DMSO_TF: 1776
分析样本数 - TAK-901: 271, DMSO_TF: 1030
过滤后基因数: 4767
⚙️ 运行PyDESeq2分析...
Fitting size factors...
/home/clab/anaconda3/envs/geneformer/lib/python3.10/site-packages/pydeseq2/dds.py:532: UserWarning: Every gene contains at least one zero, cannot compute log geometric means. Switching to iterative mode.
self.fit_size_factors(
Using None as control genes, passed at DeseqDataSet initialization
Fitting dispersions...
... done in 0.63 seconds.
Fitting MAP dispersions...
... done in 0.61 seconds. keep stucking :(
Contributor guide
First steps
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- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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- Open a pull request that references the issue number.
Research direction
Start with dds.fit_LFC() and the pydeseq2/dds.py location reported near line 532, focusing on the MAP-dispersion fitting stage after the size-factor and dispersion messages. Reproduce the DEG analysis with 4,000 tested cells and verify whether fitting completes or remains stuck, then document the cause and a confirmed resolution.
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
- 32/100