The present invention discloses methods and systems for analyzing microarray data. The method includes the general steps of providing microarray data, normalizing the data using a least trimmed squares regression, and then analyzing the normalized microarray data to obtain a desired result such as an expression profile. There is also disclosed a method of subdividing an array into subarrays before normalization. This approach provides a method for improving measurement accuracy and salvaging array data from arrays containing minor defects. Also disclosed is a Probe-Treatment-Reference (PTR) model for streamlining normalization and summarization of microarray data by allowing multiple references. Other aspects of the present invention include computer systems and computer readable media encoding methods of the present invention.