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

TitleTackling the widespread and critical impact of batch effects in high-throughput data
Publication TypeJournal Articles
Year of Publication2010
AuthorsLeek JT, Scharpf RB, Bravo HCorrada, Simcha D, Langmead B, W. Johnson E, Geman D, Baggerly K, Irizarry RA
JournalNature reviews. GeneticsNature reviews. Genetics
Volume11
Type of Article10.1038/nrg2825
Keywordsbiotechnology, Computational Biology, Genomics, Oligonucleotide Array Sequence Analysis, Periodicals as Topic, Research Design, Sequence Analysis, DNA
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.