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
lastPlot.jpeg

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
lastPlot.jpeg

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
lastPlot.jpeg

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
lastPlot.jpeg

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
lastPlot.jpeg

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
lastPlot.jpeg

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
lastPlot.jpeg

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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