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© Research
Publication : Proteomics

Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Proteomics - 01 Jan 2016

Giai Gianetto Q, Combes F, Ramus C, Bruley C, Couté Y, Burger T

Link to Pubmed [PMID] – 26572953

Proteomics 2016 Jan;16(1):29-32

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).

https://www.ncbi.nlm.nih.gov/pubmed/26572953