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jupyterlab died when Adjusting variance... #51

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brainfo opened this issue Nov 11, 2022 · 0 comments
Open

jupyterlab died when Adjusting variance... #51

brainfo opened this issue Nov 11, 2022 · 0 comments

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@brainfo
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brainfo commented Nov 11, 2022

Hi I'm using sc.external.pp.mnn_correct to correct three batches with in total 13383 obs and 6214 vars in jupyterlab.
I'm using: scanpy==1.7.2 anndata==0.8.0 umap==0.5.2 numpy==1.21.5 scipy==1.8.0 pandas==1.4.1 scikit-learn==1.0.2 statsmodels==0.13.2 python-igraph==0.9.9
with mnnpy 0.1.9.5
The kernel (always) died right after it gets in adjusting variance step
I noticed the anndata version mnnpy is using should be 0.6.22 while scanpy 1.7 uses 0.8. Could this be with the version conflict? I didn't get any error report before the crash.

Best,

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