1. Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments
- Author
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Yohann Couté, Christophe Bruley, Thomas Burger, Florence Combes, Quentin Giai Gianetto, and Claire Ramus
- Subjects
0301 basic medicine ,False discovery rate ,Computer science ,Property (programming) ,Calibration (statistics) ,Quantitative proteomics ,computer.software_genre ,Proteomics ,01 natural sciences ,Biochemistry ,Pipeline (software) ,Computer graphics ,Identifier ,010104 statistics & probability ,03 medical and health sciences ,030104 developmental biology ,Data mining ,0101 mathematics ,Molecular Biology ,computer - Abstract
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 (http://proteomecentral.proteomexchange.org/dataset/PXD002370).
- Published
- 2016