Philippe Boileau1, Nima S Hejazi1,2, Sandrine Dudoit2,3,4. 1. Graduate Group in Biostatistics. 2. Center for Computational Biology. 3. Division of Epidemiology and Biostatistics, School of Public Health. 4. Department of Statistics, University of California, Berkeley, CA 94720, USA.
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 (PCA), sparse contrastive PCA that extracts sparse, stable, interpretable and relevant biological signal. The new methodology is compared to competing dimensionality reduction approaches through a simulation study and via analyses of several publicly available protein expression, microarray gene expression and single-cell transcriptome sequencing datasets. AVAILABILITY AND IMPLEMENTATION: 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 this article is also available via GitHub. CONTACT: philippe_boileau@berkeley.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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 (PCA), sparse contrastive PCA that extracts sparse, stable, interpretable and relevant biological signal. The new methodology is compared to competing dimensionality reduction approaches through a simulation study and via analyses of several publicly available protein expression, microarray gene expression and single-cell transcriptome sequencing datasets. AVAILABILITY AND IMPLEMENTATION: 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 this article is also available via GitHub. CONTACT: philippe_boileau@berkeley.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.