library("limma")
mywt <- function  (w = 0.1) 
function(gpr) {
    flagged <- (gpr[, "Spot Flag"] < 0)
    w * flagged + (!flagged)
}
targets <- readTargets("Cartieaux/Targets.txt",sep=",")
files=targets[,1]
MA <- read.maimages(files,path="Cartieaux",source="smd",wt.fun=mywt(.1))
MA.norm <- normalizeWithinArrays(MA,method="loess",span=.2)

parameters <- cbind("Stem:Treated-Sterile"=c(1,-1,0,0),
                    "Root:Treated-Sterile"=c(0,0,1,-1))
rownames(parameters)<-c("stem treated","stem sterile","root treated","root sterile")
X <- modelMatrix(targets,parameters)
X
Comp.fit <- lmFit(MA.norm,X)
t <- Comp.fit$coefficients/Comp.fit$stdev.unscaled/Comp.fit$sigma
Comp.eb <- eBayes(Comp.fit)
Contrasts <- cbind(Inter=c(1,-1),Stem=c(1,0),root=c(0,1),Treat.Sterile=c(.5,.5))
fit2<-contrasts.fit(Comp.fit,Contrasts)
fit2<-eBayes(fit2)

toptable(Comp.eb,coef=1,number=20,adjust="fdr")
toptable(Comp.eb,coef=2,number=20,adjust="fdr")

toptable(fit2,coef=1,number=20,adjust="fdr")
toptable(fit2,coef=2,number=20,adjust="fdr")
toptable(fit2,coef=3,number=20,adjust="fdr")
toptable(fit2,coef=4,number=20,adjust="fdr")