Does Spectra accept processed expression matrix as the input?

[yizhang-zoey]

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]

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.