Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

Published online

Journal Article

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Full Text

Duke Authors

Cited Authors

  • Chen, B; Chen, M; Paisley, J; Zaas, A; Woods, C; Ginsburg, GS; Hero, A; Lucas, J; Dunson, D; Carin, L

Published Date

  • November 9, 2010

Published In

Volume / Issue

  • 11 /

Start / End Page

  • 552 -

PubMed ID

  • 21062443

Pubmed Central ID

  • 21062443

Electronic International Standard Serial Number (EISSN)

  • 1471-2105

Digital Object Identifier (DOI)

  • 10.1186/1471-2105-11-552

Language

  • eng

Conference Location

  • England