To Tweak or Not to Tweak. How Exploiting Flexibilities in Gene Set Analysis Leads to Overoptimism.

ABSTRACT: Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of genes that show enriched expression patterns between two conditions. In addition to the multitude of methods available for this task, users are typically left with many options when creating the required input and specifying the internal parameters of the chosen method. This flexibility can lead to uncertainty about the "right" choice, further reinforced by a lack of evidence-based guidance. Especially when their statistical experience is scarce, this uncertainty might entice users to produce preferable results using a "trial-and-error" approach. While it may seem unproblematic at first glance, this practice can be viewed as a form of "cherry-picking" and cause an optimistic b

SUBMITTER: Wunsch M 

PROVIDER: S-EPMC11656295 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature