FLOW CYTOMETRY:

I have 2 groups (treated and untreated) in my experiment at different time points. In the untreated group, some cell population counts are expected to become very low (even 0). This will also be accompanied by lower expression (or no expression) of specific markers. If I want to compete MFIs between groups, how should I do it? When there are no cells, FlowJo will show it as n/a in the statistics. How should I interpret this (MFI 0)?

This is a preliminary experiment. I have an N of 4 mice per group. Would it be okay to calculate the average MFI of each marker (including those n/a as zeros) and divide it by the number of cells in each corresponding population to get an MFI/cell value?

I feel kind of lost with these "n/a values."

Thanks.