Hi, I have a data frame containing the following information for genes expression levels :

    logFC(expr values 1-expr values2) expr.values1 expr.values2   rep1       rep2       rep3
    0.08054967                         10.146634    10.157469    10.039686 10.255141 10.291568

I used limma for obtaining the logFC in the first place, but original data had several replicates. Now I have generated 3 columns of "simulated" data : rep1= f(expr.values1)alpha2 , rep1= f(expr.values1)alpha2, rep1= f(expr.values1)*alpha3, where alpha are constants between (0,1). I need to get the logFC for the contrasts expr.values.1 -rep1 , expr.values.1-rep2, expr.values.1-rep3.

However when I call eBayes this time I am getting :

  Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  : 
  No residual degrees of freedom in linear model fits

How can I fix this? Is there any other possibility to compute the LogFC other than the one offered by the limma package?