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Cell cycle: ModFIT vs. FlowJo - diferent percentages outcomes on same histograms (Sep/27/2007 )

A couple of days ago I turned to flowjo (really only a beginner) for some Cell cycle analysis because I wanted to try something new (and better) than an old version of ModFIT I was already using with my FACSCalibur. Flowjo gives me more free handling in determining Gaussian peaks of G1 and G2 than ModFIT which is great for some really distorted histograms that I get with some treatments of my cells, where ModFIT is usually inadequate (don't know if I used the proper word to describe it). But then I found myself with a problem, or should I say a challenge. With ModFIT I always get the Sum of G1, S, G2 phases as 100%, whether I have a lot or none <G1 and >G2 cells. In flowjo, if I have a histogram with a lot of dead cells (usually in my treated cells) the sum of the 3 phases is not a 100%, not even close, and thus the data analyzed this way isn't comparable to ModFIT's data, or any older data I have. The real question is what should I do now? Can a flowjo be modified so that sum would always be 100%? I cannot exclude dead cells because it is a very important part of my data, and I don't want to overlook a clear error done by ModFIT in a few bad histograms.



I have the same problem with Flowjo. It doesn't give 100% of phases added together. Another problem is frequently it simply could not model my samples. I never used Modfit and don't know whether Modfit does a better job than FlowJo.