A .25mm RMS (Root Mean Square) accuracy of the ideal profile is calculated from a formula in Machinery Handbook (surface texture, RMS in the index). I would think your coordinate measuring machine would be able to do this automatically, but the formula is:
RMS Avg. = sq. rt. of ((Ya2 + Yb2 + Yn2)/n)
(the 2 means squared)
The AA average is similar, but does not square the readings and square root the average.