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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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Co-occurrence gives 'nan' if n_splits>1 in large dataset #689

Open Mena-SA-Kamel opened 1 year ago

Mena-SA-Kamel commented 1 year ago

I am re-opening this issue because I am still having problems running squidpy.gr.co_occurrence() with n_splits>1. I noticed that this has been previously discussed here and was closed without resolution. When I run on a dataset with 101510 observations while setting n_splits=1, I get an OOM error. If I don't specify an n_splits value, it sets it to 50 and I end up with all NaNs in my occurrence array. Is there a work around that you may suggest?

giovp commented 2 months ago

hi @Mena-SA-Kamel , since 1.5 it should have been fixed, could you try and install the latest version of squidpy?