[BioC] duplicateCorrelation and day effect in limma

[Pedro López Romero]

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
form: 

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

       famrep=c( 
)
 	 corfit=duplicateCorrelation(eset,ndups=1,block=famrep)

       design=model.matrix(~  - 1 +  factor(treatment))  
       
       fit=lmFit(eset,design,block=famrep,cor=corfit$consensus)
       
       
       Would be this second approach a valid one?  
       
  

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