Fix cnmf code - Githubissues

MorrissyLab / mosaicMPI

mosaicMPI: mosaic multi-resolution program integration

MIT License

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Fix cnmf code #14

Closed alyosama closed 1 year ago

verheytb commented 1 year ago

Will need to test cNMF workflow on this before merging.

[ ] Code review
[ ] Real world test

verheytb commented 1 year ago

Hi Aly, thanks for updating your PR. Can you clarify if these commits are all related to the one issue where samples/spots/cells have zeros in all the overdispersed genes? Or is this PR for multiple issues?

verheytb commented 1 year ago

Aly, I am working on testing this PR. Can you tell me about the underlying issue here: what causes this error in some datasets? It looks like you are subsetting the samples/spots/cells in both the TPM and usage matrices. Why do these samples fail in cNMF?

verheytb commented 1 year ago

Resolved this and related issues to samples with 0 counts of overdispersed genes in v1.9.3.