A major challenge in designing any automated data processing method is thinking of and anticipating all possible situations that may arise. ProCAT uses a local three by three window to correct background containing signal smears or dust speckles. This method assumes the artifacts are sparse enough so that the majority of the nine spots in the local window still provide correct measurements of the background signals. Since the median value of nine spots is used to correct the background, a few biased spots within the window will not severely affect the corrected background value. This assumption is usually valid since the percentage of spots that are either positive or whose signal is contaminated by artifacts in protein microarray experiments is generally quite low. In extreme cases where such spots are likely to be very close to each other, a larger window (five by five for example) can be used. Large artifacts such as bright speckles and incubation bubbles may affect many spots in a particular region. Since the shapes of these artifacts are variable, it is necessary to manually flag these spots initially and then remove them from future analysis. Many commercially available software packages for microarray experiments have a built in flagging function, and ProCAT will automatically discard flagged spots.