# MAVTgsa: Three methods to identify differentially expressed gene sets, ordinary least square test, Multivariate Analysis Of Variance test with n contrasts and Random forest.

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

## Man pages

- 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

## Files in this package

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 |