Can I use flow to compare flourescently labelled intracellular structures between different cells? Can I use it to compare the same cells before and after treatment? Is the mean intensity of a fluorescent signal a reasonable measure for relative quantification?
I think it would be OK to compare the fluorescence intensities before and after treatment of the same type of cell, but it would be more difficult to compare different cell types because the cell types could differ in important parameters such as size, volume, and internal composition.
Is the mean intensity of a fluorescent signal a reasonable measure for relative quantification? Yes, but you should also show the distributions, since a heterogeneous distribution could lead to misleading results if only the mean were presented.
I totally agree with Adam comments, and I think you can use the mean fluorescent intensity (MFI) for that issue.
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