multtest

Resampling-based multiple hypothesis testing

Bioconductor version: 2.8

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("multtest")

Documentation

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

Details

biocViews Microarray, DifferentialExpression, MultipleComparisons
Depends R (>= 2.9.0), methods, Biobase
Imports survival, MASS
Suggests snow
System Requirements
License LGPL
URL
Depends On Me a4Base, aCGH, BicARE, ChIPpeakAnno, gage, KCsmart, LMGene, SAGx, siggenes, webbioc
Imports Me ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector, globaltest, IsoGeneGUI, OCplus, webbioc
Suggests Me annaffy, BiocCaseStudies, ecolitk, GeneSelector, GOstats, GSEAlm, maigesPack, oneChannelGUI, pcot2, safe, SSPA, topGO, xcms
Version 2.8.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source multtest_2.8.0.tar.gz
Windows Binary multtest_2.8.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary multtest_2.8.0.tgz
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