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Last data update: 2014.03.03

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

MAVTn

R Documentation

OLS, Hottelling's T2 and MANOVA with n contrasts

Description

A gene set analysis functions for computiong the p-values for one-sided test (OLS) and two-sided test (multivariate analysis of variance). If the experimental conditions are equal to 2, the p-value for Hotelling's t square test is calculated. If the experimental conditions are great than 2, the p-value for Wilks' Lambda is deterimined and post-hoc test is reported too. The p-value for individual gene test of significant gene sets are also listed.

Usage

MAVTn(DATA, GS, MCP = 1, alpha = 0.01, nbPerm = 5000)

Arguments

`DATA`	an (m+1) x n gene expression data matrix with n samples in columns. The first row contains the information of experimental condition of each sample. The genes are expressed in the rest m rows.
`GS`	an m x k binary matrix with code (0, 1), where k is the number of gene sets. Each column represents a pre-defined gene set.
`MCP`	the choice for one of three multiple comparison methods, Dunnett = 1, Tuckey = 2, Sequential pairwise = 3.
`alpha`	the significant level
`nbPerm`	the number of permutation specified

Value

The p-values of OLS and MANOVA test are returned. If there is any significant gene set, the p values for individual genes in the gene set will be reported.

Note

R > 2.13.2

Author(s)

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

References

Chen,J.J. et al. (2007) Significance analysis of group of genes in expression profiling studies, Bioinformatics, 23, 2104.

Tsai,C.A. et al. (2009) Multivariate analysis of variance test for gene set analysis. Bioinformatics, 25, 897.

Examples


#------------simulate data matrix---------------#

data(data)
data(GS)

MAVTn(data,GS,MCP=1, nbPerm = 100)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MAVTgsa)
Loading required package: corpcor
Loading required package: foreach
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Loading required package: randomForest
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAVTgsa/MAVTn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAVTn
> ### Title: OLS, Hottelling's T2 and MANOVA with n contrasts
> ### Aliases: MAVTn
> ### Keywords: MANOVA test
> 
> ### ** Examples
> 
> 
> #------------simulate data matrix---------------#
> 
> data(data)
> data(GS)
> 
> MAVTn(data,GS,MCP=1, nbPerm = 100)
$`p value`
  GS size MANOVA p-value   adjusted p-value (FDR) adjusted p-value (FWE)
1       8           0.02                     0.04                   0.09
2       8           0.05                     0.05                   0.40
3       8           0.04                     0.05                   0.19
4       5           0.02                     0.04                   0.09
  T2 - T1 p-value T3 - T1 p-value
1            0.03            0.01
2            0.03            0.02
3            0.04            0.01
4            0.01            0.01

$`singinificant gene set`
named list()

> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>