Counting number of cells expressing a protein

[bl24]

Hello Seurat community,

I'm working on my first CITE-Seq project and I had a couple of questions regarding QC.

I've already run WNN analysis and I wanted to calculate the number of cells in each of my clusters expressing each of the surface proteins in my panel. I applied the code described in this comment: #371 (comment). I'm surprised how high the expression levels are in my result (including seeing expression in my isotype controls). And I was wondering if that is to be expected.

I was also wanting to do something analogous to mean fluorescence intensity for my data. Is this something that's possible in Seurat?