matrix_Differential_expression_analysis

library("limma")
myindir <- ""
myoutdir <- ""
setwd(myindir)

expr.df <- read.table(file = "GSE106582_series_matrix.txt", header =TRUE,comment.char = "!", row.names=1)
sampleinfo <- read.table("sampleinfo.txt",header=T)

groups <- sampleinfo$Treatment
f <- factor(groups,levels=c("CA","NO"))

design <- model.matrix(~ 0 + f)
colnames(design) <- c("CA","NO")
data.fit <- lmFit(expr.df,design)
contrast.matrix <- makeContrasts(CA-NO, levels=design)
data.fit.con <- contrasts.fit(data.fit,contrast.matrix)
data.fit.eb <- eBayes(data.fit.con)
names(data.fit.eb)

options(digits=2)
topgenes <- topTable(data.fit.eb,coef=1,number=nrow(expr.df),
                     p.value=0.05, adjust.method="BH", lfc=0)
probe <- "ILMN_1743055"
topgenes[probe, ]
#             logFC AveExpr    t P.Value adj.P.Val  B
#ILMN_1743055 -0.39       7 -8.5 5.3e-15   7.1e-14 23


filename <- colnames(expr.df)
expr <- t(expr.df["ILMN_1743055",])
GSE106582 <- cbind(sampleinfo,expr)
GSE <- rep("GSE106582",nrow=dim(GSE106582)[1])
GSE106582 <- cbind(GSE106582,GSE)
colnames(GSE106582) <- c("filename","Treatment","index","expr","GSE")

setwd(myoutdir)
write.table(GSE106582,"GSE106582.txt")