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.

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

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("multtest")

Documentation

MTP.pdf PDF
MTPALL.pdf PDF
multtest.pdf PDF R Script
Reference Manual

Details

biocViews
Depends
R , methods , Biobase
Imports
survival , MASS
Suggests
System Requirements
License LGPL
URL
Depends On Me
Imports Me
Suggests Me
Development History Bioconductor Changelog

Package Downloads

Package source multtest_2.0.0.tar.gz
Windows binary multtest_2.0.0.zip
MacOS X 10.4 (Tiger) binary multtest_2.0.0.tgz
MacOS X 10.5 (Leopard) binary multtest_2.0.0.tgz
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