selectSigGeneInt {ArrayTools}R Documentation

select differentially expressed genes from the interactionResult class

Description

select differentially expressed genes based on p value and/or fold change from the interactionResult class

Usage

selectSigGeneInt(object, pGroup = 0.05, fcGroup = 0, pMain = 0.05, fcMain = 0)

Arguments

object an interactionResult class
pGroup the p value that used to select significant genes at each level of the covariate
fcGroup the fold change value that used to select significant genes at each level of the covariate
pMain the p values that used to select significant genes among genes without any interaction effect
fcMain the fold change values that used to select significant genes among genes without any interaction effect

Value

an interactionResult

Author(s)

Xiwei Wu, Arthur Li

Examples

data(eSetExample)
design.int<- new("designMatrix", target=pData(eSetExample), covariates = c("Treatment", "Group"),
    intIndex = c(1, 2))
contrast.int<- new("contrastMatrix", design.matrix = design.int, interaction=TRUE)
result.int<- regress(eSetExample, contrast.int)
sigResult.int <- selectSigGene(result.int)
intResult <- postInteraction(eSetExample, sigResult.int, mainVar ="Treatment",
   compare1 = "Treated", compare2 = "Control")
sigResultInt <- selectSigGeneInt(intResult)

[Package ArrayTools version 1.2.1 Index]