Revisiting Fold-Change Calculation: Preference for Median or Geometric Mean over Arithmetic Mean-Based Methods

Background: Fold change is a common metric in biomedical research for quantifying group differences in omics variables. However, inconsistent calculation methods and inadequate reporting lead to discrepancies in results. This study evaluated various fold-change calculation methods aiming at a recommendation of a preferred approach. Methods: The primary distinction in fold-change calculations lies in defining group expected values for log ratio computation. To challenge method interchangeability in a “stress test” scenario, we generated diverse artificial data sets with varying distributions (identity, uniform, normal, log-normal, and a mixture of these) and compared calculated fold-changes to known values. Additionally, we analyzed a multi-omics biomedical data set to estimate to what extent the findings apply to real-world data. Results: Using arithmetic means as expected values for treatment and reference groups yielded inaccurate fold-change values more frequently than other methods, particularly when subgroup distributions and/or standard deviations differed significantly. Conclusions: The arithmetic mean method, often perceived as standard or picked without considering alternatives, is inferior to other definitions of the group expected value. Methods using median, geometric mean, or paired fold-change combinations are more robust against violations of equal variances or dissimilar group distributions. Adhering to methods less sensitive to data distribution without trade-offs and accurately reporting calculation methods in scientific reports is a reasonable practice to ensure correct interpretation and reproducibility.