As already answered: even the same machine will give different results in two different days... Why don't you simply report your results as "percentage of untreated" or as a ratio "treated/untreated"? Then you could compare the results between experiements.

wen you go for validation of specific method or test, its recommended that , the result should be reproducible apart from all variability including man power. anyways comparing MFI for a specific fluorophore with different set up is surely not appreciable. Instruments differ in settings and also laser sensitivity.

thank you for all your answers. To adjust or to fine tune the geometric mean values, what specific instrument settings has to be adjusted. As far as my knowledge goes, it is the voltage of the channel that could be adjusted. Are there any other ?

u can adjust the PMT voltages, to get your population of interest focused in a specific position. U cant go for same PMT settings for different instruments, coz as already said, the sensitivity will be differing for each instrument. In turn you can rely upon rCV% in the statistics column, or compare compensation values to get an idea of machine caliber. anyways, its recommended you can fine tune the system with Cytometer Setup and Tracking (CST) Beads, followed by compensation.

once the systems are fine tuned, ur MFI comparison will be an easy job.. hope this helps..

In fact, everybody said the same. FACS SCAN and Calibur have different sensitivities. PMT voiltage just allows you to multiply signal and to move the position of your spots. It also depends on the particular PMT. it is not comparable on SCAN and CALIBUR. In fact, it could be calculated but you need many measurements and it is pretty complicated. Why you stick on a geometric mean instead of median?