# Package multtest

## Detailed Description

Title:Resampling-based multiple hypothesis testing Description:Non-parametric bootstrap and permutation resampling-based multiple testing procedures 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). Single-step and step-wise methods are implemented. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models) are included. Results are reported in terms of adjusted p-values, confindence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.
Author:Katherine S. Pollard, Yongchao Ge, Sandrine Dudoit Maintainer:Katherine S. Pollard <kpollard@soe.ucsc.edu> Version:1.8.0 Built:R 2.2.1; i486-pc-linux-gnu; 2006-03-04 19:53:04; unix Depends:R (>= 2.1.0), methods, Biobase, survival License:LGPL Packaged:Sun Oct 16 22:24:57 2005; biocbuild

fwer2gfwer

Adjusted p-values for control of generalized FWER

**Last ouput from fwer2gfwer(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/fwer2gfwer/example.log

fwer2tppfp

Adjusted p-values for control of tail probability of the proportion of false positives

**Last ouput from fwer2tppfp(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/fwer2tppfp/example.log

fwer2fdr

Adjusted p-values for control of false discovery rate

**Last ouput from fwer2fdr(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/fwer2fdr/example.log

mt.maxT

Step-down maxT and minP multiple testing procedures

**Last ouput from mt.maxT(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/mt.maxT/example.log

mt.plot

Plotting results from multiple testing procedures

**Last ouput from mt.plot(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/mt.plot/example.log

mt.sample.teststat

Permutation distribution of test statistics and raw (unadjusted) p-values

**Last ouput from mt.sample.teststat(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/mt.sample.teststat/example.log

mt.teststat

Computing test statistics for each row of a data frame

**Last ouput from mt.teststat(). For all plots see PDF file.**

PDF output with all plots

Example code and log output is in the "Files" section, please see: multtest/mt.teststat/example.log

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