The present invention provides methods for analyzing multi-channel profiles. In the method of the invention, systematic cross-profile (cross-experiment) errors among a plurality of multi-channel profiles having a common reference channel are estimated using profiles of the common reference channel. The cross-profile errors are then removed from profiles of the experiment channels, e.g., by subtracting the error from the experiment profile. The obtained error-corrected experiment channel data can then be used in comparison with each other, e.g., in generating virtual differential profiles between pairs of experiment channels. The method of the invention is particularly useful in analyzing multi-channel expression profiles obtained in microarray measurements.