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.

Author | Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J. Chen |

Date of publication | 2014-07-02 13:48:35 |

Maintainer | Chih-Yi Chien <92354503@nccu.edu.tw> |

License | GPL-2 |

Version | 1.3 |

**data:** Example data for MAVTn

**design.matrix:** Design matrix

**GS:** Example data for MAVTn

**GSTplot:** GST plot

**Hott2:** Hottelling's T square

**ma.estimate:** Estimate of the coefficients

**MAVTgsa-package:** OLS and Multivariate Analysis of Variance test for gene set...

**MAVTn:** OLS, Hottelling's T2 and MANOVA with n contrasts

**MAVTp:** Random Forests-based procedure

**minp:** P-values adjustment in permutation

**Tols:** Ordinary Least Square test

**Wilksn:** Wilk's Lambda for n-group multiple comparisons

MAVTgsa

MAVTgsa/NAMESPACE

MAVTgsa/data

MAVTgsa/data/GS.rda

MAVTgsa/data/data.rda

MAVTgsa/R

MAVTgsa/R/MAVTgsa.R
MAVTgsa/MD5

MAVTgsa/DESCRIPTION

MAVTgsa/man

MAVTgsa/man/GSTplot.Rd
MAVTgsa/man/MAVTgsa-package.Rd
MAVTgsa/man/MAVTn.Rd
MAVTgsa/man/Tols.Rd
MAVTgsa/man/Wilksn.Rd
MAVTgsa/man/MAVTp.Rd
MAVTgsa/man/data.Rd
MAVTgsa/man/minp.Rd
MAVTgsa/man/design.matrix.Rd
MAVTgsa/man/Hott2.Rd
MAVTgsa/man/ma.estimate.Rd
MAVTgsa/man/GS.Rd
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