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Pré-publication, Document de travail

Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters

Lucas Etourneau 1, 2 Nelle Varoquaux 2 Thomas Burger 3
2 TIMC-TrEE - Translational microbial Evolution and Engineering
TIMC - Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525
Abstract : Abstract In proteomic differential analysis, FDR control is often performed through a multiple test correction ( i . e ., the adjustment of the original p-values). In this protocol, we apply a recent and alternative method, based on so-called knockoff filters. It shares interesting conceptual similarities with the target-decoy competition procedure, classically used in proteomics for FDR control at peptide identification. To provide practitioners with a unified understanding of FDR control in proteomics, we apply the knockoff procedure on real and simulated quantitative datasets. Leveraging these comparisons, we propose to adapt the knockoff procedure to better fit the specificities of quantitive proteomic data (mainly very few samples). Performances of knockoff procedure are compared with those of the classical Benjamini-Hochberg procedure, hereby shedding a new light on the strengths and weaknesses of target-decoy competition.
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Pré-publication, Document de travail
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https://hal.archives-ouvertes.fr/hal-03373565
Contributeur : Thomas Burger Connectez-vous pour contacter le contributeur
Soumis le : lundi 11 octobre 2021 - 15:24:57
Dernière modification le : jeudi 4 novembre 2021 - 11:36:41

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Lucas Etourneau, Nelle Varoquaux, Thomas Burger. Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters. 2021. ⟨hal-03373565⟩

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