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The problem of identifying significantly differentially expressed genes for replicated microarray experiments is accepted as significant and has been tackled by several researchers. Patterns from Gene Expression (PaGE) and q-values are two of the well-known approaches developed to handle this problem. This paper proposes a powerful approach to handle this problem. We first propose a method for estimating the prior probabilities used in the first version of the PaGE algorithm. This way, the problem definition of PaGE stays intact and we just estimate the needed prior probabilities. Our estimation method is similar to Storey's estimator without being its direct extension. Then, we modify the problem formulation to find significantly differentially expressed genes and present an efficient method for finding them. This formulation increases the power by directly incorporating Storey's estimator. We report the preliminary results on the BRCA data set to demonstrate the applicability and effectiveness of our approach.
q-values, significantly differentially expressed genes, microarray, pattern generation, PaGE.

R. Alhajj, F. Polat and O. Abul, "A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. , pp. 220-231, 2006.
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