Dear all

I am having Affymetrix Dataset(.cel) with replicates for different time points.(1hr- 4cntrl,4expt, 4hrs-4cntrl,4expts, and 1day-4cntrl and 4 expt). Do i want to run limma separately for each time point or Can i run limma simultaneously for all time points by assigning them as a separate group. i tried both. But it gives different result. If there is any wrong in my question,plz apologise me,since am new to bioconductor.

If all of these samples are from the same study/experiment, you should run everything together. It increases the residual d.f. (i.e., the information available to estimate the residual variance), which improves power for detecting DE.