Tackling the widespread and critical impact of batch effects in high-throughput data

Jeffrey T. Leek, Robert B. Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W. Evan Johnson, Donald Geman, Keith Baggerly, Rafael A. Irizarry

Research output: Contribution to journalReview articlepeer-review

Abstract

High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published studies and our own analyses, we argue that batch effects (as well as other technical and biological artefacts) are widespread and critical to address. We review experimental and computational approaches for doing so.

Original languageEnglish (US)
Pages (from-to)733-739
Number of pages7
JournalNature Reviews Genetics
Volume11
Issue number10
DOIs
StatePublished - Oct 14 2010

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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