Cosbin: cosine score-based iterative normalization of biologically diverse samples

Abstract

Motivation Data normalization is essential to ensure accurate inference and comparability of gene expression measures across samples or conditions. Ideally, gene expression data should be rescaled based on consistently expressed reference genes. However, to normalize biologically diverse samples, most commonly used reference genes exhibit striking expression variability, and size-factor or distribution-based normalization methods can be problematic when the amount of asymmetry in differential expression is significant. Results We report an efficient and accurate data-driven method—Cosine score based iterative normalization (Cosbin) - to normalize biologically diverse samples. Based on the Cosine scores of cross-condition expression patterns, the Cosbin pipeline iteratively eliminates asymmetric differentially expressed genes, identifies consistently expressed genes, and calculates sample-wise normalization factors. We demonstrate the superior performance and enhanced utility of Cosbin compared with six representative peer methods using both simulation and real multi-omics expression datasets. Implemented in open-source R scripts and specifically designed to address normalization bias due to significant asymmetry in differential expression across multiple conditions, the Cosbin tool complements rather than replaces the existing methods and will allow biologists to more accurately detect true molecular signals among diverse phenotypic groups. Availability The R Scripts of Cosbin pipeline is freely available at https://github.com/MinjieSh/Cosbin. Supplementary information Supplementary data are available at Bioinformatics Advances online.