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

multtest

Resampling-based multiple hypothesis testing

Bioconductor version: 2.13

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 gladstone.ucsf.edu>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("multtest")

 

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

Details

biocViews	DifferentialExpression, Microarray, MultipleComparisons, Software
Version	2.18.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier
License	LGPL
Depends	R (>= 2.10), methods, Biobase
Imports	survival, MASS, stats4
Suggests	snow
System Requirements
URL
Depends On Me	a4Base, aCGH, BicARE, ChIPpeakAnno, iPAC, KCsmart, LMGene, PREDA, REDseq, SAGx, siggenes, webbioc
Imports Me	ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector, globaltest, IsoGeneGUI, OCplus, phyloseq, REDseq, RTopper, synapter, webbioc
Suggests Me	annaffy, BiocCaseStudies, ecolitk, factDesign, GeneSelector, GOstats, GSEAlm, maigesPack, MmPalateMiRNA, oneChannelGUI, pcot2, topGO, xcms

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	multtest_2.18.0.tar.gz
Windows Binary	multtest_2.18.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	multtest_2.18.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats