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wenjie1991/read_affy_cel.R

Created September 11, 2018 02:51
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read_affy_cel.R
## download and install package
# source("http://bioconductor.org/biocLite.R")
# biocLite("oligo")
library(oligo)
## read cel files
dir <- tcltk::tk_choose.dir(caption = "Please choose input fold contain cel")
raw <- list.celfiles(dir, full.names=TRUE)
affyGeneFS <- read.celfiles(raw)
## apply normalization
norm <- rma(affyGeneFS, target = "probeset")
## wrtie expression data into file named "normalized.xls"
write.table(exprs(norm), file = "normalized.xls", sep = "\t", quote = F)
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