What is Fluorescence Compensation?
Briefly, in any experimental system where two or more fluorochromes (multi-color analysis) are used to characterize the cells of interest, fluorescence compensation must be considered. Fluorescence compensation is the mathematical subtraction of the fluorescence due to one fluorochrome from the fluorescence due to another fluorochrome. This is necessary because emission spectra from two fluorochromes can overlap. For this reason, in a sample that contains (for example) both fluorescein and phycoerythrin (two of the most common fluorochromes), fluorescence due to FITC (for example) will be detected by the electronics that are set up to detect fluorescence due to phycoerythrin. If this were not subtracted from the phycoerythrin fluorescence, the latter would be spuriously high. To determine the correct amount of fluorescence compensation, cells stained with only one fluorochrome-conjugated antibody are analyzed individually. This must be done for each of the fluorochromes used in the exp
