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Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments
- Source :
- PROTEOMICS. 16:29-32
- Publication Year :
- 2016
- Publisher :
- Wiley, 2016.
-
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).
- 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
Subjects
Details
- ISSN :
- 16159853
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- PROTEOMICS
- Accession number :
- edsair.doi...........87f294a4f1e8f1881fe2f8c718bc4f89