[kosulin]

There is more: intonation is also action dependant! When you fret the string, you stretch it making it longer and thinner compared to the distance between fret and saddle and to the thickness of an open string, and the higher the action and the higher the postion is, the bigger this difference is, and as a result, the sound is usually more flat on high frets with high action. Some luthiers compensate fret positions to neutralize this effect for recommended action. These calculations are not trivial. You can Google for dissertation of Ernst Frisch who proposed a system for measuring the right fret locations.