TY - JOUR T1 - Tackling the widespread and critical impact of batch effects in high-throughput data JF - Nature reviews. GeneticsNature reviews. Genetics Y1 - 2010 A1 - Leek, Jeffrey T. A1 - Scharpf, Robert B. A1 - Héctor Corrada Bravo A1 - Simcha, David A1 - Langmead, Benjamin A1 - Johnson, W. Evan A1 - Geman, Donald A1 - Baggerly, Keith A1 - Irizarry, Rafael A. KW - biotechnology KW - Computational Biology KW - Genomics KW - Oligonucleotide Array Sequence Analysis KW - Periodicals as Topic KW - Research Design KW - Sequence Analysis, DNA AB - 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. VL - 11 N1 - http://www.ncbi.nlm.nih.gov/pubmed/20838408?dopt=Abstract ER -