Spot defects detection in cDNA microarray images

Abstract

Bad quality spots should be filtered out at early steps in microarray analysis to avoid noisy data. In this paper we implement quality control of individual spots from real microarray images. First of all, we consider the binary classification problem of detecting bad quality spots. We propose the use of ensemble algorithms to perform detection and obtain improved accuracies over previous studies in the literature. Next, we analyze the untackled problem of identifying specific spot defects. One spot may have several faults simultaneously (or none of them) yielding a multi-label classification problem. We propose several extra features in addition to those used for binary classification, and we use three different methods to perform the classification task: five independent binary classifiers, the recent Convex Multi-task Feature Learning (CMFL) algorithm and Convex Multi-task Independent Learning (CMIL). We analyze the Hamming loss and areas under the receiver operating characteristic (ROC) curves to quantify the accuracies of the methods. We find that the three strategies achieve similar results leading to a successful identification of particular defects. Also, using a Random forest-based analysis we show that the newly introduced features are highly relevant for this task.