Does Spectra accept processed expression matrix as the input?

dpeerlab / spectra

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

MIT License

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Does Spectra accept processed expression matrix as the input? #41

Open yizhang-zoey opened 4 months ago

yizhang-zoey commented 4 months ago

As input, the algorithm receives a normalized cell-by-gene count matrix.

Because I want to use the integrated scRNA data, I only have the processed cell-by-gene expression matrix. Will it affect the results if I use a processed expression matrix instead of a count matrix as the input?

russellkune commented 3 months ago

Hi my expectation is that this should be fine. We didn't try on integrated data, we actually applied it pre-integration and found programs that capture batch effects.