1. A method of modifying image data from a biological probe array to determine a final feature intensity for a feature, wherein said feature is comprised of a set of pixels said method comprising: a. obtaining sample image data comprising a set of observed pixel values from the biological probe array wherein each observed pixel value is a measure of the intensity for a single pixel in the set of pixels and calculating an observed feature intensity for said feature from the observed pixel values; b. estimating a theoretical pixel intensity for each pixel in the set of pixels using: (i) an empirically based transfer function that relates the distance of each pixel from the feature center with an intensity value that is proportional to the observed feature intensity, (ii) a background intensity value for said feature, and (iii) an estimated feature intensity for said feature; c. determining an optimized multiplicative error function using a multiplicative error function and a standard deviation function, wherein said multiplicative error function comprises calculating multiplicative error values that are a ratio of the observed pixel values and said theoretical pixel intensity and the standard deviation function comprises comparing the multiplicative error values to a selected value and removing pixels having multiplicative error values that are greater than the selected value; d. determining an updated feature intensity by adjusting the observed feature intensity by an update factor, wherein said update factor is calculated by assigning a weight value for each pixel in the set of pixels and using the weight values to define a weight function and multiplying the optimized multiplicative error function with the weight function; and e. using the updated feature intensity as the final feature intensity if the updated feature intensity has converged to a unique value or repeating steps b to e using the updated feature intensity as the estimated feature intensity.