tTest: Use t Test to Compare Two Groups

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Use a (modified) t test to compare two groups

Usage

tTest(object, groups, probe2gene = TRUE)

Arguments

object	ExpressionSet object
groups	string indicating the name of the variable of the phenoData containing the group information
probe2gene	logical; if TRUE Affymetrix probeset IDs are translated into gene symbols; if FALSE no such translation is conducted

Details

For multiple testing the mt.rawp2adjp function of package multtest is used.

Value

Object of class "tTest", a data frame with the following columns

gSymbol	Gene Symbol
p	p-value of the difference between the groups
logRatio	Log ratio of the expression between the groups
pBH	p-value of the difference between the groups, with Benjamini-Hochberg multiplicity correction
tStat	Student t-statistic of the different between groups

Author(s)

Willem Talloen, Tobias Verbeke

See Also

rowttests in rowFtests

Examples

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
  tTestRes <- tTest(object = ALL,	groups = "BTtype", probe2gene = TRUE)
  volcanoPlot(tTestRes)  
}

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.