Multi-study Factor Analysis

Abstract: We introduce a novel class of factor analysis methodologies for the joint analysis of multiple studies. The goal is to separately identify and estimate 1) common factors shared across multiple studies, and 2) study-specific factors. We develop a fast Expectation Conditional-Maximization algorithm for parameter estimates and we provide a procedure for choosing the common and specific factor. We present simulations evaluating the performance of the method and we illustrate it by applying it to gene expression data in ovarian cancer. In both cases, we clarify the benefits of a joint analysis compared to the standard factor analysis. We hope to have provided a valuable tool to accelerate the pace at which we can combine unsupervised analysis across multiple studies, and understand the cross-study reproducibility of signal in multivariate data.