FACS is very popular in quantification of cell surface antigen by using fluorescent labelled beads as the standard. When comparing to different cell lines with variable cell sizes, I think FACS method is limited because the size of cells will give variations (such as two cell lines (to say one is 1um and the other is 10um) with exactly same copies of antigen per cell will give different MFI). I wish some experts in FACS field can give me more suggestions about that.
Thanks very much for your answer. It is very helpful.
Usually the beads with known fluorescent molecule number were used as the standard to quantify the antigen copies in cell surface. When comparing to the same cell type, it still make sense even the absolute copies are not exactly correct. But when comparing between different cell lines with dramatic size differences, the biology is not related to the calculated antigen copies in cell surface.
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