ArrayTools (version 1.32.0)

selectSigGeneInt: 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

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)