[BioC] duplicateCorrelation and day effect in limma

Pedro López Romero plopez at cnic.es
Wed Jun 28 13:57:09 CEST 2006

Dear list, 

I have a simple doubt concerning how I should deal with the *replicate day*
effect using limma. 
It is clear that I have a *day effect* in my data that it has to be taken
into account in the model. I am using 2 different model specifications and I
do not know if one of them is correct. 

a) A first solution is simply to include in the model the *day effect* as an
additional fixed effect. I will assume that there is not interaction between
*day effect* and *treatment effect*, so my design matrix will be of the

    design=model.matrix(~  - 1 +  factor(treatment) + factor(day) )  
b) My question is if I can take into account the *day effect* as random
effect using duplicateCorrelation. 


       design=model.matrix(~  - 1 +  factor(treatment))  
       Would be this second approach a valid one?  

I will appreciate any comment on this.-     
Thanks a lot.- 

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