Bridging the False Discovery Gap

Article Biology

Competition-based control of the false discovery proportion

Dong Luo et al.

Summary: Recently, Barber and Candes proposed a general framework for controlling the false discovery rate (FDR) based on knockoffs. However, existing FDR control methods like target-decoy competition (TDC) suffer from the problem of FDP exceeding the desired level alpha. In this study, we introduce a new procedure called FDP-SD that rigorously controls the FDP in the knockoff/TDC setup and demonstrates improved power in both simulated and real data compared to a recently published framework.

BIOMETRICS (2023)

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Article Biochemical Research Methods

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

Andy Lin et al.

Summary: The analysis of shotgun proteomics data often involves controlling the false discovery rate (FDR) through target-decoy competition (TDC). This study highlights the limitations of PSM-level FDR estimation and proposes focusing on peptide-level analysis instead. Three methods for peptide-level TDC are investigated, with the PSM-and-peptide method found to be the most powerful, resulting in a 17% increase in discovered peptides at the 1% FDR threshold compared to the PSM-only method.

JOURNAL OF PROTEOME RESEARCH (2022)

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Article Genetics & Heredity

Use ggbreak to Effectively Utilize Plotting Space to Deal With Large Datasets and Outliers

Shuangbin Xu et al.

Summary: ggbreak is an R package based on ggplot2 that helps users effectively tackle data visualization issues with large datasets, enhancing the interpretative capability of the data.

FRONTIERS IN GENETICS (2021)

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Article Biochemical Research Methods