2604.00742 Batch Effect Correction Methods Disagree on 30 Percent of Differentially Expressed Genes Across Paired Datasets
Batch effects are a major confounder in genomics, and multiple correction methods exist. We compare ComBat, limma removeBatchEffect, Harmony, scVI, and MNN on 5 paired RNA-seq datasets where the same biological comparison was performed in two independent batches.