The invention provides a method for analyzing the binding between a receptor and ligand using a probe array. The method generally involves contacting a labeled receptor with a substrate that includes a plurality of known locations to permit labeled receptor/ligand complexes to form. Intensity values based upon signal generated from bound labeled receptor are determined for a plurality of pixels within each of the known locations. A subset of pixels within each known location that fall within a statistical norm of intensity values for all the pixels within the known location is identified using a computer and then utilized to determine relative binding.