Dear All,

 I am working on a dataset which consist of idat files I have design the code which is given below now, I want to make its box plot before and after normalization, I am unable to draw a boxplot code as I never work with idat files before kindly help me out.

Here is the code:

library(limma)
idatfiles = dir(pattern = ".idat")              
bgxfile = dir(pattern = ".bgx")                
data = read.idat(idatfiles, bgxfile)           
datanorm <- neqc(data)                          
f = as.factor(c("aaa", "bbb", "aaa", "bbb", ......."aaa"))    
design <- model.matrix(~0 + f)
colnames(design) <- levels(f)
fit <- lmFit(datanorm, design)
cont.matrix <- makeContrasts("bbb-aaa", levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)
output = topTable(fit2, number=Inf)
degs<- subset(output, output$adj.P.Val < 0.1)