Batch effect

library(affy)

wk.dir <- "E:\\CEL\\BrainCancer\\U133B\\76samples"
rma.file <- "Brain.U133B.76.txt"

####################
# RMA
setwd(wk.dir)
data.rma<-justRMA()
write.exprs(data.rma, file=rma.file)


####################
# Check batch effect
source("E:\\R_lib\\Microarray.R")
get.files.info()
#!!!Edit the color manually in file "files.info.user.batch.txt"
check.batch.effect(rma.file)


####################
# RMA for each batch
rma.by.batch()