NPM: latent batch effects correction of omics data by nearest-pair matching.

ABSTRACT:

Motivation

Batch effects (BEs) are a predominant source of noise in omics data and often mask real biological signals. BEs remain common in existing datasets. Current methods for BE correction mostly rely on specific assumptions or complex models, and may not detect and adjust BEs adequately, impacting downstream analysis and discovery power. To address these challenges we developed NPM, a nearest-neighbor matching-based method that adjusts BEs and may outperform other methods in a wide range of datasets.

Results

We assessed distinct metrics and graphical readouts, and compared our method to commonly used BE correction methods. NPM demonstrates the ability in correcting for BEs, while preserving biological differences. It may outperform other methods based on multiple metric

SUBMITTER: Zito A 

PROVIDER: S-EPMC11925496 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature