Exploring high-dimensional biological data with sparse contrastive principal component analysis

Abstract

Motivation: Statistical analyses of high-throughput sequencing data have re-shaped the biological sciences. In spite of myriad advances, recovering interpretable biological signal from data corrupted by technical noise remains a prevalent open problem. Several classes of procedures, among them classical dimensionality reduction techniques, and others incorporating subject-matter knowledge, have provided effective advances; however, no procedure currently satisfies the dual objectives of recovering stable and relevant features simultaneously. Results: Inspired by recent proposals for making use of control data in the removal of unwanted variation, we propose a variant of principal component analysis that extracts sparse, stable, interpretable, and relevant biological signal. The new methodology is compared to competing dimensionality reduction approaches through a simulation study as well as via analyses of several publicly available protein expression, microarray gene expression, and single-cell transcriptome sequencing datasets. Availability: A free and open-source software implementation of the methodology, the scPCA R package, is made available via the Bioconductor Project. Code for all analyses presented in the paper are also made available via GitHub.