Nothing
############### Differentiall Expression method##########
diffExp <- function(object,comparison=NULL,volcanoPlot=FALSE,...){
state <- object@phenoData$Treatment
f <- factor(state)
design <- model.matrix(~0+f)
colnames(design) <- levels(f)
contrast.matrix <- limma::makeContrasts(comparison,levels=design)
fit <- limma::lmFit(object@qData,design)
fit <- limma::contrasts.fit(fit, contrast.matrix)
ebayes <- limma::eBayes(fit)
if(volcanoPlot==TRUE){
jpeg("Valcanoplot.jpg")
limma::volcanoplot(ebayes, coef=1, highlight=0, names=fit$genes$ID, xlab="Log Fold Change", ylab="Log Odds", pch=16, cex=0.35)
dev.off()
}
object@diffExp <- limma::topTable(ebayes,number = Inf)
new("NcmsProcessData",object)
}
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