MFI subtraction

Dear Flowers,

Sorry for a never-ending question regarding comparison of MFI in a test sample vs. MFI in a negative control, but I get confused by one of my client.... He wants to compare intracellular marker expression between two subpopulations of T lymphocytes. The way I have compared MFI (mean fluorescence intensity) between the two so far was the ratio of the value in the test tube against the value in the isoclonic. However, this math shows absolutely no difference between populations... So, the client of mine insists to subtract the MFI value in the control from the value in the test sample, showing as a proof, some papers from high-impacted journals, where such calculation was performed. Is it correct?

Thanks for clarification this issue.

Jarek Baran