There are few antibodies like CD54, CD88, for which only a fraction of my neutrophil population is positive and not all. So should I report the MFI of only positive population or MFI of entire population?
this depends on your goal. The MFI in general show your protein expression per gated cell. If you want a unbiased view and show that those populations are unregulated you show the MFI of the entire population. If your goal is to show that even in your positive populations you have a higher expression of the antigenes than you might consider reporting the positive population. Hope that helps.
MFI gives a better idea about the population you want to show or discuss. So its better you show MFI of both the populations in order to differentiate between positive and total population.