[BioC] duplicateCorrelation and day effect in limma
naomi at stat.psu.edu
Thu Jun 29 04:41:03 CEST 2006
You could do it either way, and your use of duplicateCorrelation is correct.
At 07:57 AM 6/28/2006, Pedro López Romero wrote:
>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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Naomi S. Altman 814-865-3791 (voice)
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