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?

Thanks,

Jeremy

Hi Jeremy,

I meet the same problem, I also want to use limma package to deal with my SILAC data, but I really confused what codes should I use. Should I build a design matrix?

If you could reply me, so appreciated it!

Thanks so much! Best, Peiru