RE: input data for PHATE

[vravik]

Hey guys,

I'm trying to understand how to appropriately use MAGIC and PHATE for my analysis.
When I perform dimensionality reduction with PCA/ UMAP after imputing gene counts, the data representation I get are vastly different. I was thus wondering if it'd be appropriate to run PHATE on the imputed counts data, rather than normalized raw counts. I tried searching the web for answers but haven't been able to find a good explanation.

Thank you