Is there any need to set up a design or contrast matrix using limma ebayes on ratiometric replicates? I have three replicate ratios that are log2 transformed. I'm running ebayes:
data = read.csv(paste(inpath,fname,sep=""),header=T,stringsAsFactors=F,na.strings="NaN",sep="\t")
fit = lmFit(data[,c("rep1","rep2","rep3")]))
fit2 = eBayes(fit)
tt = topTable(fit2, adjust="BH",number=Inf,confint=T,sort.by='none')
Where "rep 1-3" are the columns containing the ratio measurements. Is this correct?