FAMT swMATH ID: 11123 Software Authors: David Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg Description: R package FAMT: Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data. The method proposed in this package takes into account the impact of dependence on the multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered in the model is chosen to reduce the false discoveries variance in multiple tests. The model parameters are estimated thanks to an EM algorithm. Adjusted tests statistics are derived, as well as the associated p-values. The proportion of true null hypotheses (an important parameter when controlling the false discovery rate) is also estimated from the FAMT model. Graphics are proposed to interpret and describe the factors. Homepage: http://cran.r-project.org/web/packages/FAMT/index.html Source Code: https://github.com/cran/FAMT Dependencies: R Related Software: leapp; R; FADA; GitHub; Eigenstrat; FarmTest; rda; WGCNA; glmnet; impute; Excel; mixOmics; armada; sma; RankGene; ClustOfVar; mixfdr; denoiseR; ruv; missForest Cited in: 33 Publications Standard Articles 2 Publications describing the Software, including 1 Publication in zbMATH Year A factor model approach to multiple testing under dependence. Zbl 1205.62071Friguet, Chloé; Kloareg, Maela; Causeur, David 2009 all top 5 Cited by 60 Authors 6 Causeur, David J. 5 Fan, Jianqing 5 Friguet, Chloé 4 Roquain, Étienne 3 Delattre, Sylvain 3 Perthame, Émeline 2 Jeng, X. Jessie 2 Kloareg, Maela 2 Storey, John D. 2 Verzelen, Nicolas 2 Zhao, Haibing 2 Zhou, Wen-Xin 1 Bastien, B. 1 Blum, Yuna 1 Bodnar, Taras 1 Bodwin, Kelly 1 Bose, Koushiki 1 Boukhobza, Taha 1 Carpentier, Alexandra 1 Chen, Xi 1 Chen, Xiongzhi 1 Chiang, Derek Y. 1 Cui, Xinping 1 Deng, Lu 1 Desai, Keyur H. 1 Devijver, Emilie 1 Dumond, H. 1 Gégout-Petit, Anne 1 Gerard, David 1 Gu, Weijie 1 Han, Xu 1 Houée-Bigot, Magalie 1 Ke, Yuan 1 Kuan, Pei Fen 1 Lee, Yuh-Shiow 1 Leek, Jeffrey T. 1 Li, Zhonghua 1 Liao, Yuan 1 Liu, Han 1 Muller-Gueudin, Aurélie 1 Nobel, Andrew B. 1 Ormerod, John T. 1 Owen, Art B. 1 Peddada, Shyamal D. 1 Reiß, Markus 1 Sheu, Ching-Fan 1 Stephens, Matthew 1 Stewart, Michael 1 Sun, Qiang 1 Sun, Yunting 1 Thiebaut, C. 1 Wang, Kaizheng 1 Wang, Weichen 1 Yu, Chang 1 Yu, Weichang 1 Zelterman, Daniel 1 Zhang, Nancy Ruonan 1 Zhong, Yiqiao 1 Zhu, Ziwei 1 Zi, Xue-Min all top 5 Cited in 18 Serials 6 The Annals of Statistics 4 Journal of the American Statistical Association 3 Journal of Multivariate Analysis 3 The Annals of Applied Statistics 2 Communications in Statistics. Theory and Methods 2 Statistical Applications in Genetics and Molecular Biology 2 Statistics and Computing 1 Biometrical Journal 1 Biometrics 1 Statistical Science 1 Communications in Statistics. Simulation and Computation 1 Computational Statistics and Data Analysis 1 Statistica Sinica 1 Bernoulli 1 Journal of Applied Statistics 1 Journal of Machine Learning Research (JMLR) 1 Journal de la Société Française de Statistique 1 Journal of Statistical Distributions and Applications all top 5 Cited in 7 Fields 32 Statistics (62-XX) 7 Biology and other natural sciences (92-XX) 4 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year