Multiple testing corrections in quantitative proteomics: A useful but blunt tool. Issue 18 (September 2016)

• Record Type: Journal Article
• Authors: Pascovici, Dana; Handler, David C. L.; Wu, Jemma X.; Haynes, Paul A.
• Other Names: Haynes Paul A. guestEditor.; Stein Stephen E. guestEditor.; Washburn Michael P. guestEditor.
• Is Part Of: Proteomics. Volume 16:Issue 18(2016)
• Page Start: 2448
• Page End: 2453
• Publication Date: 2016-09
• Subjects: FDR -- Multiple testing corrections -- Shot gun proteomics; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.201600044
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract : Multiple testing corrections are a useful tool for restricting the FDR, but can be blunt in the context of low power, as we demonstrate by a series of simple simulations. Unfortunately, in proteomics experiments low power can be common, driven by proteomics‐specific issues like small effects due to ratio compression, and few replicates due to reagent high cost, instrument time availability and other issues; in such situations, most multiple testing corrections methods, if used with conventional thresholds, will fail to detect any true positives even when many exist. In this low power, medium scale situation, other methods such as effect size considerations or peptide‐level calculations may be a more effective option, even if they do not offer the same theoretical guarantee of a low FDR. Thus, we aim to highlight in this article that proteomics presents some specific challenges to the standard multiple testing corrections methods, which should be employed as a useful tool but not be regarded as a required rubber stamp.