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Resampling-based multiple hypothesis testing

Bioconductor version: Release (3.1)

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.

Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit

Maintainer: Katherine S. Pollard <kpollard at>

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PDF   Reference Manual


biocViews DifferentialExpression, Microarray, MultipleComparison, Software
Version 2.24.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License LGPL
Depends R (>= 2.10), methods, Biobase
Imports survival, MASS, stats4
Suggests snow
Depends On Me a4Base, aCGH, BicARE, iPAC, KCsmart, LMGene, PREDA, rain, REDseq, SAGx, siggenes, webbioc
Imports Me ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector, globaltest, IsoGeneGUI, mAPKL, metabomxtr, nethet, OCplus, phyloseq, REDseq, RTopper, synapter, webbioc
Suggests Me annaffy, BiocCaseStudies, ecolitk, factDesign, GeneSelector, GGtools, GOstats, GSEAlm, maigesPack, MmPalateMiRNA, oneChannelGUI, pcot2, PECA, topGO, xcms
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