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Gene-specific exponent-corrected normalization for library size in bulk RNA-seq

Correcting for library size is an essential step in bulk RNA-seq analyses, as differences in sequencing depth across samples can obscure biological signal with technical noise. Wh

GIST

Correcting for library size is an essential step in bulk RNA-seq analyses, as differences in sequencing depth across samples can obscure biological signal with technical noise. While numerous normalization methods and model-based strategies have been proposed, we demonstrate here that library size-normalized counts and differential expression results obtained from such widely adopted approaches often remain strongly correlated with library size in large-scale RNA-seq experiments. Through a systematic analysis of over 100 publicly available GEO and TCGA RNA-seq datasets with raw count data, we show that library size association is observed for a substantial proportion of genes even after state-of-the-art library size correction approaches recommended by leading normalization tools. To address this issue, we propose gecco, a gene-specific exponent-corrected normalization method for RNA-seq counts that incorporates library size directly into the statistical framework via a gene-specific correction term, rather than applying a uniform adjustment factor across all genes. This formulation generalizes existing normalization approaches and yields normalized counts that are free of residual library size effects.

Clinical Editorial

bioRxiv (Biomedical Preprints) published a clinical update in Research Highlights on 09 Jul 2026. The item focuses on Gene-specific exponent-corrected normalization for library size in bulk RNA-seq. Review the original article for the full source wording and details.

Original source: https://www.biorxiv.org/content/10.64898/2026.07.04.736167v1?rss=1