Robust DNA microarray image analysis

Abstract.

DNA microarrays are an increasingly important tool that allow biologists to gain insight into the function of thousands of genes in a single experiment. Common to all array-based approaches is the necessity to analyze digital images of the scanned DNA array. The ultimate image analysis goal is to automatically quantify every individual array element (spot), providing information about the amount of DNA bound to a spot. Irrespective of the quantification strategy, the preliminary information to extract about a spot includes the mapping between its location in the digital image and its possibly distorted position in the spot array (gridding). We present a gridding approach divided into a spot-amplification step (matched filter), a rotation estimation step (Radon transform), and a grid spanning step. Quantification of the spots is performed by robustly fitting of a parametric model to pixel intensities with the help of M-estimators. The main advantage of parametric spot fitting is its ability to cope with overlapping spots. If the goodness-of-fit is too bad, a semiparametric spot fitting is employed. We show that our approach is superior to simple quantification strategies such as averaging of the pixel intensities. The system was extensively tested on 1740 images resulting from two DNA libraries.