multtest swMATH ID: 8262 Software Authors: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit Description: multtest: Resampling-based multiple hypothesis testing. Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. Homepage: http://www.bioconductor.org/packages/release/bioc/html/multtest.html Dependencies: R Related Software: R; Bioconductor; gcrma; qvalue; vcd; mvtnorm; Phyloseq; structSSI; fastICA; MASS (R); fda (R); SAS; affy; haplo.stats; SNPStats; SNPassoc; Stata; SAS/STAT; modeltools; exactRankTests Cited in: 18 Publications all top 5 Cited by 36 Authors 4 Dudoit, Sandrine 4 Van der Laan, Mark Johannes 3 Aoshima, Makoto 3 Yata, Kazuyoshi 2 Greenwood, Mark C. 2 Miecznikowski, Jeffrey C. 1 Bellante, G. J. 1 Carey, Vincent J. 1 Causeur, David J. 1 Friguet, Chloé 1 Gaile, Daniel P. 1 Gentleman, Robert 1 Gilbert, Houston N. 1 Gold, David 1 Holmes, Susan P. 1 Holodov, Dmitri 1 Huber, Wolfgang 1 Irizarry, Rafael A. 1 Keles, Sunduz 1 Kloareg, Maela 1 Lawrence, R. L. 1 Liu, Song 1 Lourenço, Vanda M. 1 Mair, Patrick 1 Pires, Ana M. 1 Pollard, Katherine S. 1 Powell, S. L. 1 Repasky, K. S. 1 Sankaran, Kris 1 Scrucca, Luca 1 Segal, Mark Robert 1 Serafini, Alessio 1 Shepherd, Lori 1 Tuglus, Catherine 1 Vsevolozhskaya, O. A. 1 Vsevolozhskaya, Olga all top 5 Cited in 11 Serials 4 Statistical Applications in Genetics and Molecular Biology 2 Communications in Statistics. Theory and Methods 2 Computational Statistics and Data Analysis 2 Journal of Computational and Graphical Statistics 1 Biometrical Journal 1 Journal of Multivariate Analysis 1 Statistics & Probability Letters 1 Methodology and Computing in Applied Probability 1 The Annals of Applied Statistics 1 Use R! 1 Statistics for Biology and Health all top 5 Cited in 6 Fields 17 Statistics (62-XX) 6 Biology and other natural sciences (92-XX) 1 General and overarching topics; collections (00-XX) 1 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) Citations by Year