Hello,
I want to present my cytometry data using histograms/scatter dot plots. I thought I should focus on MFI to export my data. However, in some cases where I see a change in the percentage of population that is stained, the MFI remains unchanged (see attached example). I used MFI median and geometric mean. Am I using a unadapted parameter to measure MFI? What should I use instead of median and geometric mean? Should I use a different method other than MFI? If yes, what method can you suggest?
Thank you,
Best,
Martin
So... when you use the mean/median of the gated population, it is only on the gated population. So despite the fact that your % positive went up, if the spread of that data is the same as the other, the mean/median won't change.
If you want to use MFI instead of percent positive, use the mean/median for the ENTIRE population.
using the median or geometric mean is correct for MFI. however, in your sample, the spread of gated population is the same regardless of how many cells are in it. As such it would be better to use percent positive instead of MFI. This parameter will give true reflection of upregulated expression of your marker
best,
Martin Schnitzler first of all please compare the gated X-median. Secondly and more importantly, It entirely depends upon the question you are trying to answer. For example, a change in %age (let's say a decrease) of labelled cells indicates the loss of cognate molecules available for binding on more number of cells (Vis-a-vis before the decrease in %age of labelled cells), however, the MFI calculation is still based only on the number of labelled cells e.g. 1697 vs 66 in your case. Thus please be focussed on MFI unless the loss of cognate molecules available for binding is biologically relevant to you. Please comment.
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