It has been recognized that for appropriately ordered data, hidden Markov models (HMM) with local false discovery rate (FDR) control can increase the power to detect significant associations. For many high-throughput technologies, the cost still limits their application. Two-stage designs are attractive, in which a set of interesting features or biomarkers is identified in a first stage and then followed up in a second stage. However, to our knowledge, no two-stage FDR control with HMMs has been developed. In this paper, we study an efficient HMM–FDR-based two-stage design, using a simple integrated analysis procedure across the stages. Numeric studies show its excellent performance when compared to available methods. A power analysis method is also proposed. We use examples from microbiome data to illustrate the methods.
CITATION STYLE
Zhou, Y. H., Brooks, P., & Wang, X. (2018). A Two-Stage Hidden Markov Model Design for Biomarker Detection, with Application to Microbiome Research. Statistics in Biosciences, 10(1), 41–58. https://doi.org/10.1007/s12561-017-9187-y
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