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SBRG / pymodulon

Python package for analyzing and visualizing iModulons
MIT License
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Incorrect/bad dimensionality recommendation #44

Closed sapoudel closed 3 years ago

sapoudel commented 3 years ago

The notebook sometimes recommends incorrect/bad dimensionality. In some cases, it will recommend high dimensionality even when the number of robust components drop sharply (see image). In these high dimensional decomposition (almost) all iModulons have near 0 activities in all samples.

image

avsastry commented 3 years ago

This is fixed in the modulome-workflow version here: https://github.com/avsastry/modulome-workflow/tree/main/4_optICA The dimensionality search is integrated in with the rest of the code as well.