2015/08/13 by Vegard Nygaard, Einar Andreas Rødland, Eivind Hovig · 1 voice · 2 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · #Bioinformatics and Genomic Networks #Gene expression and cancer classification #Statistical Methods and Inference
paper · pdf · doi:10.1093/biostatistics/kxv027
openalex publication_date 2015/08/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
Removal of, or adjustment for, batch effects or center differences is generally required when such effects are present in data. In particular, when preparing microarray gene expression data from multiple cohorts, array platforms, or batches for later analyses, batch effects can have confounding effects, inducing spurious differences between study groups. Many methods and tools exist for removing batch effects from data. However, when study groups are not evenly distributed across batches, actual group differences may induce apparent batch differences, in which case batch adjustments may bias, usually deflate, group differences. Some tools therefore have the option of preserving the difference between study groups, e.g. using a two-way ANOVA model to simultaneously estimate both group and batch effects. Unfortunately, this approach may systematically induce incorrect group differences in downstream analyses when groups are distributed between the batches in an unbalanced manner. The scientific community seems to be largely unaware of how this approach may lead to false discoveries.