I'm using Limma to normalize Affy data sets from 2 experimental studies performed using microarray ,
To check whether the steps that I follow is correct, I am checking whether the box plot that I obtain after processing the RAW file is the same as the boxplot obtained from GSE. GSE:
library(Biobase) library(GEOquery) eset <- getGEO('GSE20966')[] boxplot(exprs(eset), outline=FALSE)
library(gcrma) library(limma) downloadedAffyFiles <- list.files(path = "../Data/GSE20966_RAW/", pattern = "CEL.gz$",full.names=TRUE) AffyData <- ReadAffy(filenames = downloadedAffyFiles) eset <- gcrma(AffyData) Data <- exprs(eset) boxplot(exprs(eset), outline=FALSE)
Since both the plots are different, I understand the difference comes out of the normalization method that is used. Could someone suggest what changes have to be made in the above syntax? How can I set the method of normalization?