Sensitized-emission fluorescence resonance energy transfer (FRET) detection method based on three-channel fluorescence microscopy is widely used. Several FRET algorithms, such as NFRET, FRETN, FR, FRETR, and FC/Df, are developed recently to quantitatively gauge and compare FRET signals between different experimental groups. However, the algorithms are difficult to choose and interpret. In this letter, we optimize the suitable yellow fluorescent protein (YFP) to cyan fluorescent protein (CFP) concentration ratio range for the above FRET algorithms. We also test the effect of YFP-to-CFP concentration ratio on the calculated energy transfer efficiency E and use the optimized FRET algorithms in the analysis of fas-associated protein with death domain (FADD) self-association directly in living cells.