Entering edit mode
2.6 years ago
Aki
▴
10
I am using limma to analyze Agilent's single color arrays to find differentially expressed genes, using the following procedure.
targets <- limma::readTargets("targets.txt")
project <- limma::read.maimages(targets,source="agilent", green.only=TRUE)
project.bgc <- backgroundCorrect(project, method="normexp", offset=50)
project.NormData <-normalizeBetweenArrays(project.bgc,method="quantile")
design <- paste(targets$Target, sep="")
design <- factor(design)
comparisonmodel <- model.matrix(~0+design)
colnames(comparisonmodel) <- levels(design)
project.fit <- lmFit(project.NormData, comparisonmodel)
project.fit.eBayes <- eBayes(project.fit)
CaseControl <- makeContrasts(TR-Control, levels=comparisonmodel)
CaseControl.fitmodel <- contrasts.fit(project.fit.eBayes, CaseControl)
CaseControl.fitmodel.eBayes <- eBayes(CaseControl.fitmodel)
The problem is that I don't know how to make a heatmap.
Does anyone tell a way to do this?
