A robust removing unwanted variation-testing procedure via -divergence

DOI10.1111/BIOM.13002MaRDI QIDQ5214526zbMATH OpenOpenAlexWikidataFDO

Authors Hung Hung

Publication date 7 February 2020

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1711.01674

zbMATH Keywords

multiple hypothesis testingrobustnessunwanted variation\(\gamma\)-divergencenegative control genesremoving unwanted variation

Mathematics Subject Classification ID

Nonparametric robustness (62G35) Applications of statistics to biology and medical sciences; meta analysis (62P10) Paired and multiple comparisons; multiple testing (62J15)

Abstract: Identification of differentially expressed genes (DE-genes) is commonly conducted in modern biomedical researches. However, unwanted variation inevitably arises during the data collection process, which could make the detection results heavily biased. It is suggested to remove the unwanted variation while keeping the biological variation to ensure a reliable analysis result. Removing Unwanted Variation (RUV) is recently proposed for this purpose by the virtue of negative control genes. On the other hand, outliers are frequently appear in modern high-throughput genetic data that can heavily affect the performances of RUV and its downstream analysis. In this work, we propose a robust RUV-testing procedure via gamma-divergence. The advantages of our method are twofold: (1) it does not involve any modeling for the outlier distribution, which is applicable to various situations, (2) it is easy to implement in the sense that its robustness is controlled by a single tuning parameter gamma of gamma-divergence, and a data-driven criterion is developed to select $gamma$. In the Gender Study, our method can successfully remove unwanted variation, and is able to identify more DE-genes than conventional methods.

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Cited in

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• Unifying and generalizing methods for removing unwanted variation based on negative controls

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