1. A method for analyzing gene expression data obtained from a plurality of microarrays having a plurality of probes, wherein the plurality of probes includes mismatch (MM) probe pairs having a mismatch value and perfect match (PM) probe pairs having a perfect match value, the method comprising the steps of: obtaining image data corresponding to scanned microarrays, the image data for each scanned microarray comprising an image corresponding to the scanned probe intensities, scan date, and at least one chip identifier; storing the image data for each scanned microarray in at least one database; applying an automated quality control process, comprising the steps of in a processor, processing the image data by applying at least a portion of a plurality of image processing metrics comprising algorithms adapted to identify one or more defects selected from the group consisting of haze, bright artifacts, dim artifacts, crop circles, snow, misalignment, grid misalignment, high background intensity, saturation, scratches, cracks; flagging any identified defects; assigning a pass/fail status to each microarray based upon identified defects, if any; storing the processed image data in the at least one database, the processed image data comprising the scanned probe intensities, the scan date, the at least one chip identifier, the pass/fail status, the applied image processing metrics, and the identified defects, if any; providing a user interface for searching the at least one database by selecting at least one chip parameter from the group consisting of scan date, the at least one chip identifier, the pass/fail status and the plurality of image processing metrics; and displaying the results of the search.