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© Research
Publication : Proteomics

Uses and misuses of the fudge factor in quantitative discovery proteomics

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Proteomics - 01 Jul 2016

Giai Gianetto Q, Couté Y, Bruley C, Burger T

Link to Pubmed [PMID] – 27272648

Proteomics 2016 Jul;16(14):1955-60

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 s0 . 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.

https://www.ncbi.nlm.nih.gov/pubmed/27272648