Uses and misuses of the fudge factor in quantitative discovery proteomics. Issue 14 (21st July 2016)

• Record Type: Journal Article
• Authors: Giai Gianetto, Quentin; Couté, Yohann; Bruley, Christophe; Burger, Thomas
• Is Part Of: Proteomics. Volume 16:Issue 14(2016)
• Page Start: 1955
• Page End: 1960
• Publication Date: 2016-07-21
• Subjects: Bioinformatics -- Differential abundance -- Discovery proteomics -- Statistical analysis; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.201600132
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract : Selecting proteins with significant differential abundance is the cornerstone of many relative quantitative proteomics experiments. To do so, a trade‐off between p ‐value thresholding and fold‐change thresholding can be performed because of a specific parameter, named fudge factor, and classically noted s 0 . We have observed that this fudge factor is routinely turned away from its original (and statistically valid) use, leading to important distortion in the distribution of p ‐values, jeopardizing the protein differential analysis, as well as the subsequent biological conclusion. In this article, we provide a comprehensive viewpoint on this issue, as well as some guidelines to circumvent it.