Set up methods, analysis methods and monitoring methods for capillary gel arrays are provided which rigorously determine the number of capillaries for which standards should be used and/or the capillaries in which standards should not be considered and/or for which performance is impaired. The invention includes methods for monitoring capillary gel array performance in which the capillary gel array performs, on a plurality of occasions, a size based separation on an unknown sample in one or more capillaries, a size based separation on a second standard in those one or more capillaries, and a size based separation on a standard in one or more other capillaries, comprising comparing the results of the sample to the results of the standards in which variation in a characteristic of the results from the capillaries provided with the standard are considered with time and variation of the characteristic outside a predetermined position to determine if one or more of the capillaries of the array are providing reduced performance. The invention provides rigour to the results obtained from capillary gel array analysis and prevents analysis being carried out on arrays which have developed problems or broken down.