library(limma)
targets <- readTargets("SwirlSample.txt")
RG <- read.maimages(targets$FileName, source="spot", sep="\t", path="./")
RG$genes <- readGAL()
RG$printer <- getLayout(RG$genes)
imageplot(log2(RG$R[,1]), RG$printer, low="white", high="red")
plotPrintTipLoess(RG)
MA <- normalizeWithinArrays(RG, method="printtiploess")
plotPrintTipLoess(MA)
boxplot(MA$M~col(MA$M),names=colnames(MA$M))
MA <- normalizeBetweenArrays(MA)
design <- c(-1,1,-1,1)
boxplot(MA$M~col(MA$M),names=colnames(MA$M))
fit <- lmFit(MA, design)
fit <- eBayes(fit)
print(topTable(fit, adjust="fdr", sort.by="B", number=10))