Inferential Clustering Approach for Microarray Experiments with Replicated Measurements
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Robust Bayesian Clustering for Replicated Gene Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Affymetrix high-density oligonucleotide microarrays measure the expression of DNA transcripts using probesets, i.e. multiple probes per transcript. Usually, these multiple measurements are transformed into a single probeset expression level before data analysis proceeds; any information on variability is lost. In this paper we demonstrate how individual probe measurements can be used in a statistic for differential expression. Furthermore, we show how this statistic can serve as a criterion for clustering microarrays. Results: A novel clustering algorithm using this maximum significance criterion is demonstrated to be more efficient with the measured data than competing techniques for dealing with repeated measurements, especially when the sample size is small. Availability: MATLAb source code can be found at http://ict.ewi.tudelft.nl/~dick Contact: D.deRidder@ewi.tudelft.nl