How to use counts from an integrated experiment for downstream tools?

[alexwskh]

Hello,

I just want to check my understanding and make sure that I'm doing the right thing. I have an integrated seurat object from 5 scRNAseq experiments. I would like to use the escape package for single cell gene score enrichment analysis found here which requires the counts. From my understanding, as long as I have run the "PrepSCTFindMarkers", I should have corrected counts that have been scaled for the integrated object as a whole instead of the individual experiments.

Is that correct or am I missing something fundamental here? Thank you,