selectSigGeneInt: select differentially expressed genes from the...

In ArrayTools: geneChip Analysis Package

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)

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.