A method and apparatus for compensating for non-linearities due to pivot bearing friction when determining embedded runout correction values during partial self-servo write of a disk drive is disclosed. In one embodiment, the disk drive includes a disk surface having a track written thereon and the track has some written-in runout. The written-in runout that is associated with high-frequencies is determined using a first technique. The written-in runout for the track that is associated with low frequencies is determined using a second technique. Results from the two techniques are combined in order to determine embedded runout correction values for the track when partial self-servo writing, in order to reduce error propagation when writing additional tracks.