R::Normalization::Affymetrix .CEL file::using RMA

In R, set your working directory to where the .CEL files are contained (File->Change dir) OR from the R prompt:

>setwd("your full directory here with quotation marks")

At the prompt, install BiocLite by copy-pasting the code below(includes the Affy packages needed for normalization):

>source("http://bioconductor.org/biocLite.R")
>biocLite()

Load Affy package for normalization:

>library(affy)

Load the .CEL files and do RMA normalization:

>Data<-ReadAffy()
>eset<-rma(Data)

Write a tab-delimited file of the normalized data.

>write.exprs(eset, file="insertFileNameHereWithQuotes.txt", sep="\t")

Optional: QC Plots and Analysis

Install and load the made4 package:

>biocLite("made4")
>library(made4)

Get a quick overview of the data: hierarchical clustering dendrogram, boxplot, histogram.

>overview(eset)