I have a question about my agilent microarray data.
It includes before & after infection data of the same individuals and also replicates of non-infected other individuals as a kind of control to these infected ones . There are 15 individuals and thus 30 microarray files. I am using "limma" package to read and normalize them. However, i have doubts if i should use the codes below to identifiy genes differently expressed, because when i cluster the datasets, the replicates do not group together:
RG_2= backgroundCorrect(z, method="minimum")
SibShip = factor(targets_paired$SibShip)
Treat = factor(targets_paired$Treatment, levels=c("Not Inf.","Infected"))
design = model.matrix(~SibShip+Treat)
fit = lmFit(MA.exp_log, design)
fit = eBayes(fit)
In this case, should I analyze the data by just grouping as Infected & Non-infected?
Thank you in advance.