A disk drive is disclosed that estimates a sinusoidal error in a wedge time period due to eccentricity in the disk rotating to generate eccentricity compensation values. During a write operation a head is positioned over a target data sector within a target track, a write clock frequency is set using an eccentricity compensation value corresponding to the target data sector, and data is written to the target data sector using the write clock frequency. In this manner, the eccentricity compensation value adjusts the write clock frequency to better optimize the linear bit density from the inner to outer diameter tracks.