We present here a method to compare the mathematical descriptions of DNA migration per pulse as a function of pulse time. It is based on obtaining robust estimates and variances of DNA reorientation time, migration velocities during and after DNA reorientation; and on the statistical comparisons of these estimates. We demonstrated an equal description for the migration per pulse of each DNA molecule separated under identical conditions in clamped homogeneous electric field (CHEF) and miniCHEF chambers. However, miniCHEF resolved the patterns in shorter times, because it uses thinner samples. The relationship between sample thickness and CHEF run time is also presented.