Nonparametric bootstrap and permutation resamplingbased multiple testing procedures (including empirical Bayes methods) for controlling the familywise error rate (FWER), generalized familywise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrapbased null distribution are implemented (centered, centered and scaled, quantiletransformed). Singlestep and stepwise methods are available. Tests based on a variety of t and Fstatistics (including tstatistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with tstatistics, 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 pvalues, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.
Package details 


Author  Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit 
Bioconductor views  DifferentialExpression Microarray MultipleComparison 
Maintainer  Katherine S. Pollard <[email protected]> 
License  LGPL 
Version  2.33.0 
Package repository  View on GitHub 
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