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Abstract:
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Cancer 'omics datasets involve widely varying sizes and scales, measurement variables, and correlation structures. An overarching scientific goal in cancer research is the invention of general statistical techniques that can cleanly sift the signal from the noise in identifying genomic signatures of the disease across a set of experimental or biological conditions. We propose BayesDiff, a nonparametric Bayesian approach based on a novel class of first order mixture models, called the Sticky Poisson-Dirichlet process or multicuisine restaurant franchise. The BayesDiff methodology flexibly utilizes information from all the measurements and adaptively accommodates any serial dependence in the data, accounting for the inter-probe distances, to perform simultaneous inferences on the variables. The technique is applied to analyze the motivating colorectal cancer DNA methylation dataset. In simulation studies, we demonstrate the effectiveness of the BayesDiff procedure relative to existing techniques for differential DNA methylation. Returning to the motivating dataset, we detect the genomic signature for four subtypes of colorectal cancer.
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