A note on the false discovery rate and inconsistent comparisons between experiments

Bioinformatics
Roger HigdonEugene Kolker

Abstract

The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies. However, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple comparison corrections it may be an inappropriate way to compare results across experiments. This article uses several examples based on gene-expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other measures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high-throughput studies because data are often re-used for different objectives, including comparing common elements across many experiments. No single error rate or data summary may be appropriate for all of the different objectives.

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Citations

Mar 27, 2012·Analytical and Bioanalytical Chemistry·Giulia GonnelliLennart Martens
Mar 1, 2013·Big Data·Roger HigdonEugene Kolker
Aug 12, 2009·Omics : a Journal of Integrative Biology·Jukka HiissaTero Aittokallio
Jun 24, 2010·Omics : a Journal of Integrative Biology·Roger HigdonEugene Kolker
Dec 20, 2013·Journal of Proteome Research·Roger HigdonEugene Kolker
Jun 10, 2014·Omics : a Journal of Integrative Biology·Elizabeth MontagueEugene Kolker
Aug 6, 2008·Journal of Cellular Physiology·Bradley P CoeWan L Lam
May 26, 2011·Journal of Proteomics·Eugene KolkerNatali Kolker
Nov 19, 2014·Nucleic Acids Research·Elizabeth MontagueEugene Kolker
Dec 10, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Millissia Ben MaamarMichael K Skinner
Nov 6, 2020·Environmental Health : a Global Access Science Source·Jennifer L M ThorsonMichael K Skinner
Oct 12, 2020·Environmental Research·Millissia Ben MaamarMichael K Skinner
Apr 13, 2021·Environmental Epigenetics·Jennifer L M ThorsonMichael K Skinner

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