[BioC] How to get and save normalized data from limma

[Wang, Jixin]

Dear All,

I want to use the normalized signal intensities data to do hierarchical clustering. But I don’t know how to save the normalized data from LIMMA. 


Below is the code:

library(limma)
setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO")
targets <- readTargets("equi.txt")
targets
RG <- read.maimages(targets$FileName, source="genepix")
RG
 
MA <- normalizeWithinArrays(RG)
 
MA <- normalizeBetweenArrays(MA,method="scale")
 
design <- c(-1,1,-1,1,-1,1)
fit <- lmFit(MA,design)
 

fit <- eBayes(fit)
topTable(fit,number=500,adjust="BH")

volcanoplot(fit)

Thanks a lot,

Jixin