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Transmission properties of data amplitude modulation (AM) and frequency modulation (FM) in radio-over-fiber (RoF) system are studied numerically. The influences of fiber dispersion and nonlinearity on different microwave modulation schemes, including double side band (DSB), single side band (SSB) and optical carrier suppression (OCS), are investigated and compared. The power penalties at the base station (BS) and the eye opening penalties of the recovered data at the end users are both calculated and analyzed. Numerical simulation results reveal that the power penalty of FM can be drastically decreased due to the larger modulation depth it can achieve than that of AM. The local spectrum broadening around subcarrier microwave frequency of AM due to fiber nonlinearity can also be eliminated with FM. It is demonstrated for the first time that the eye openings of the FM recovered data can be controlled by its modulation depths and the coding formats. Negative voltage encoding format was used to further decrease the RF frequency thus increase the fluctuation period considering their inverse relationship.