library(Biobase)
library(BiocGenerics)
library(affy)
library(limma)

filename = list.files("CCLEpaxOVrna")
dir = paste("./CCLEpaxOVrna/",filename,sep="")
n = length(dir)
data = ReadAffy(filenames=filename[1] )
for (i in 2:n){ new.data = ReadAffy(filenames = filename[i])
data = merge(data,new.data)}
aaa<-rma(data)
aa2<-exprs(aaa)

control<-aa2[,c(2,3,4,7,10,12,17,19,21,26)]
LPS<-aa2[,-c(2,3,4,7,10,12,17,19,21,26)]
length(colnames(control))
length(colnames(LPS))
design <- model.matrix(~ -1+factor(c(1,1,1, 2,2,2)))
colnames(design) <- c("control", "LPS")
fit <- lmFit(aa2, design)
contrast.matrix <- makeContrasts(control-LPS, levels=design)
fit <- eBayes(fit)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
results<-decideTests(fit2, method="global", adjust.method="BH", p.value=0.01, lfc=1.5)
summary(results)