Journal
PROTEOMICS
Volume 16, Issue 1, Pages 29-32Publisher
WILEY
DOI: 10.1002/pmic.201500189
Keywords
False discovery rate; Relative quantification experiments; Statistical significance
Funding
- ProFI project [ANR-10-INBS-08]
- RNAGermSilence project [ANR-13-BSV2-0012]
- Agence Nationale de la Recherche (ANR) [ANR-13-BSV2-0012] Funding Source: Agence Nationale de la Recherche (ANR)
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In MS-based quantitative proteomics, the FDR control (i.e. the limitation of the number of proteins that are wrongly claimed as differentially abundant between several conditions) is a major postanalysis step. It is classically achieved thanks to a specific statistical procedure that computes the adjusted p-values of the putative differentially abundant proteins. Unfortunately, such adjustment is conservative only if the p-values are well-calibrated; the false discovery control being spuriously underestimated otherwise. However, well-calibration is a property that can be violated in some practical cases. To overcome this limitation, we propose a graphical method to straightforwardly and visually assess the p-value well-calibration, as well as the R codes to embed it in any pipeline. All MS data have been deposited in the ProteomeXchange with identifier PXD002370 ().
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