Dapple: Improved Techniques for Finding Spots on DNA Microarrays

Abstract

A key step in experiments using DNA microarrays is locating the thousands of individual spots in a scanned array image.Each spot provides quantitative information about a distinct DNA sequence, so it is imperative that spots be found and quantitated accurately. Spot finding is complicated by varia- tions in the positions and sizes of spots and by the presence of artifacts and background noise in microarray images.We describe Dapple, a new spot finding implementation for microarrays on glass slides. Dapple finds spots using mor- phological information which is robust to both variation and artifacts. It achieves high spot finding throughput and ac- curacy by learning to evaluate the quality of candidate spots from examples supplied by the user. Dapple’s techniques are useful for improving the accuracy of data acquisition from DNA microarrays.