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.

[YuliaInn]

Do you have any updates on this? My data is integrated with CCA. Which assay and slot should I use as input? @yizhang-zoey Did you run spectra on your integrated data? How did it go?
Thank you

[YuliaInn]

@russellkune could you please explain this? You used a pre-integration count matrix (log or raw?) and what did you find? What kind of programs did capture the batch effects? Are they in global annotations?
thank you