Last data update: 2014.03.03
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MAVTgsa
Package: MAVTgsa
Type: Package
Title: Three methods to identify differentially expressed gene sets,
ordinary least square test, Multivariate Analysis Of Variance
test with n contrasts and Random forest.
Version: 1.3
Date: 2014-05-27
Author: Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J. Chen
Maintainer: Chih-Yi Chien <92354503@nccu.edu.tw>
Depends: R (>= 2.13.2), corpcor, foreach, multcomp, randomForest, MASS
Description: This package is a gene set analysis function for one-sided test (OLS), two-sided test (multivariate analysis of variance).
If the experimental conditions are equal to 2, the p-value for Hotelling's t^2 test is calculated.
If the experimental conditions are great than 2, the p-value for Wilks' Lambda is determined and post-hoc test is reported too.
Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented.
The program computes the p-values and FDR (false discovery rate) q-values for all gene sets.
The p-values for individual genes in a significant gene set are also listed.
MAVTgsa generates two visualization output: a p-value plot of gene sets (GSA plot) and a GST-plot of the empirical distribution function of the ranked test statistics of a given gene set.
A Random Forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes.
License: GPL-2
LazyData: Yes
Repository: CRAN
Packaged: 2014-06-30 03:41:28 UTC; pelly
NeedsCompilation: no
Date/Publication: 2014-07-02 13:48:35
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MAVTgsa' ...
** package 'MAVTgsa' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'MAVTgsa'
finding HTML links ... done
GS html
GSTplot html
Hott2 html
MAVTgsa-package html
MAVTn html
MAVTp html
Tols html
Wilksn html
data html
design.matrix html
ma.estimate html
minp html
** building package indices
** testing if installed package can be loaded
* DONE (MAVTgsa)
Making 'packages.html' ... done
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