Exploratory methods to integrate multisource data

Eric F. Lock, Andrew B. Nobel

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

In biomedical research, a growing number of measurement platforms and technologies are being used to assess diverse but related information on a set of common samples. This motivates integrative methods for multisource data, in which multiple data sets are derived from a common set of objects. This chapter addresses exploratory methods for multisource data. We discuss the need for flexible approaches that simultaneously model the dependence and the heterogeneity of the sources and describe two such methods in detail: joint and individual variation explained (JIVE) and Bayesian consensus clustering (BCC). JIVE is a general decomposition of variation for multisource data. The decomposition consists of three terms: a low-rank approximation capturing joint variation across sources, low-rank approximations for structured variation individual to each source, and residual noise. JIVE quantifies the amount of joint variation between sources, reduces dimensionality, and allows for visual exploration of joint and individual structure. BCC is a tool to cluster a set of objects based on multisource data. The model permits a separate clustering of the objects for each source that adhere loosely to an overall clustering.We describe a Bayesian framework for simultaneous estimation of the source-specific and overall clusterings. We illustrate JIVE and BCC with applications to publicly available data from the Cancer Genome Atlas.

Original languageEnglish (US)
Title of host publicationIntegrating Omics Data
PublisherCambridge University Press
Pages242-268
Number of pages27
ISBN (Electronic)9781107706484
ISBN (Print)9781107069114
DOIs
StatePublished - Jan 1 2015

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