CellChat on Integrated Seurat Data

[me-orlov]

Hello,

I would like to use CellChat on data that consists of several samples individually processed with SCT and integrated in Seurat. I am wondering whether anyone has done this, or knows the answers to the following:

Which assay would I use for the CellChat? I assume the "integrated" assay is out, as it contains slightly positive/negative values for genes with zero expression? The RNA assay is problematic because the different samples have different sequencing depths. Would the merged object (with multiple SCT models) be all right, once corrected for sequencing depth?

Thank you for your time and your wonderful software.