You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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?
The text was updated successfully, but these errors were encountered:
yizhang-zoey
changed the title
Does Spectra only accept normalized count matrix as a input?
Does Spectra accept processed expression matrix as a input?
Mar 15, 2024
yizhang-zoey
changed the title
Does Spectra accept processed expression matrix as a input?
Does Spectra accept processed expression matrix as the input?
Mar 15, 2024
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.
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
@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
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?
The text was updated successfully, but these errors were encountered: