Volcano plot for mean fluorescence intensity (flow cytometry) data

Question

[jackarnestad]

I want to make a volcano plot based on the log fold change between two classes of samples which I have flow cytometry data on (over 50 markers). Most of the tutorials for volcano plots for RNA seq start with differential expression, but they require raw count matrices rather than the equivalent normalized matrix I am starting with.

How would you suggest calculating log fold change and p value for this data? From there, plotting a volcano plot is easy.

Thanks, Jack

[Devon Ryan]

What exactly does your data look like?