selectSigGeneInt {ArrayTools} | R Documentation |
select differentially expressed genes based on p value and/or fold change from the interactionResult class
selectSigGeneInt(object, pGroup = 0.05, fcGroup = 0, pMain = 0.05, fcMain = 0)
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 |
an interactionResult
Xiwei Wu, Arthur Li
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)