Optimal Selection of Microarray Analysis Methods Using a Conceptual Clustering Algorithm

Abstract. The rapid development of methods that select over/under expressed genes from microarray experiments have not yet matched the need for tools that identify informational profiles that differentiate between experimental condi-tions such as time, treatment and phenotype. Uncertainty arises when methods devoted to identify significantly expressed genes are evaluated: do all microar-ray analysis methods yield similar results from the same input dataset? do dif-ferent microarray datasets require distinct analysis methods?. We performed a detailed evaluation of several microarray analysis methods, finding that none of these methods alone identifies all observable differential profiles, nor subsumes the results obtained by the other methods. Consequently, we propose a proce-dure that, given certain user-defined preferences, generates an optimal suite of statistical methods. These solutions are optimal in the sense that they constitute partial ordered subsets of all possible method-associations bounded by both, the most specific and the most sensitive available solution.