A Factor Model Approach to Multiple Testing Under Dependence

Friguet, Chloé; Kloareg, Maëla; Causeur, David

doi:10.1198/jasa.2009.tm08332

Cited by 137 publications

(198 citation statements)

References 23 publications

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“…The factorial analysis for multiple testing (FAMT) approach described in Friguet et al (2009) was adopted to increase statistical power between a variation in the transcription level of an individual gene and the contamination level of a given contaminant as well as some morphometric measurements (age and condition index (C.I.)). Since length is highly correlated with age, it was not added to the model.…”

Section: Methodsologymentioning

confidence: 99%

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Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Bertucci

Pierron

Thébault

et al. 2017

Environ Sci Pollut Res

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The freshwater pearl mussel Margaritifera margaritifera is one of the most threatened freshwater bivalves worldwide. In this study, we aimed (i) to study the processes by which water quality might affect freshwater mussels in situ and (ii) to provide insights into the ecotoxicological significance of water pollution to natural populations in order to provide necessary information to enhance conservation strategies. M. margaritifera specimens were sampled in two close sites located upstream or downstream from an illegal dumping site. The renal transcriptome of these animals was assembled and gene transcription determined by RNA-seq. Correlations between transcription levels of each single transcript and the bioaccumulation of nine trace metals, age (estimated by sclerochronology), and condition index were determined in order to identify genes likely to respond to a specific factor. Amongst the studied metals, Cr, Zn, Cd, and Ni were the main factors correlated with transcription levels, with effects on translation, apoptosis, immune response, response to stimulus, and transport pathways.However, the main factor explaining changes in gene transcription appeared to be the age of individuals with a negative correlation with the transcription of retrotransposon-related genes. To investigate this effect further, mussels were classified into three age classes. In young, middle-aged and old animals, transcription levels were mainly explained by Cu, Zn and age, respectively. This suggests differences in the molecular responses of this species to metals during its lifetime that must be better assessed in future ecotoxicology studies.

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Section: Methodsologymentioning

confidence: 99%

“…In order to counter this issue, we then used a factor analysis for multiple testing (FAMT ;Friguet et al 2009) approach to explore the transcriptomic effect of individual pollutants, age, and C.I. to identify genes that are likely to be related to one single factor.…”

Section: Effects Of Individual Factors On Gene Expression In Kidneymentioning

confidence: 99%

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Bertucci

Pierron

Thébault

et al. 2017

Environ Sci Pollut Res

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“…The factor-adjusted multiple testing (FAMT) procedure is a recently developed method for large-scale simultaneous hypothesis testing in high correlation situations (Friguet, Kloareg, & Causeur, 2009). Dependence is formalized as latent variables in the FAMT procedure,and multiple hypothesis testing is performed with adjustment for latent variables.…”

Section: Introductionmentioning

confidence: 99%

“…The present study aims to adapt the FAMT procedure under dependence (Friguet et al, 2009) to the analysis of ERP waveforms. We propose a dynamic version of the FAMT procedure to account for the high correlations among ERP observations over time and perform simulation studies to illustrate the advantages of using this novel procedure for managing the multiplicity problem in ERP data analysis.…”

Section: Introductionmentioning

confidence: 99%

“…We first introduce the BH procedure for multiple testing, followed by a discussion of the FAMT procedure under dependence method (Friguet et al, 2009). We perform two simulation studies: one to illustrate the impact of dependence on the performance of the BH procedure and another to assess and compare the performance of our dynamic FAMT procedure against that of the BH procedure.…”

Section: Introductionmentioning

confidence: 99%

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A factor-adjusted multiple testing procedure for ERP data analysis

et al. 2012

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Event-related potentials (ERPs) are now widely collected in psychological research to determine the time courses of mental events. When event-related potentials from treatment conditions are compared, often there is no a priori information on when or how long the differences should occur. Testing simultaneously for differences over the entire set of time points creates a serious multiple comparison problem in which the probability of false positive errors must be controlled, while maintaining reasonable power for correct detection. In this work, we extend the factor-adjusted multiple testing procedure developed by Friguet, Kloareg, and Causeur (Journal of the American Statistical Association, 104, 1406-1415, 2009) to manage the multiplicity problem in ERP data analysis and compare its performance with that of the Benjamini and Hochberg (Journal of the Royal Statistical Society B, 57, 289-300, 1995) false discovery rate procedure, using simulations. The proposed procedure outperformed the latter in detecting more truly significant time points, in addition to reducing the variability of the false discovery rate, suggesting that corrections for mass multiple testings of ERPs can be much improved by modeling the strong local temporal dependencies.

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Introduction to Statistical Methods for Complex Systems

Mary‐Huard

Robin

2011

Handbook of Statistical Systems Biology

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A Factor Model Approach to Multiple Testing Under Dependence

Cited by 137 publications

References 23 publications

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

A factor-adjusted multiple testing procedure for ERP data analysis

Introduction to Statistical Methods for Complex Systems

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