Dear members,

I have the same design as in section 8.2 Paired samples in Limma user guide (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.182.2271&rep=rep1&type=pdf). Treatment or control is apply on the same cell.
The recommendation is to perform an paired t-test (equivalent to a fixed model) but in my mind, I will choose random effect and use duplicatecorrelation in lmfit. Results are totaly different.
What are the main aspect to choose between fixed or random.
thanks for any comments
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