Question: duplicateCorrelation and day effect in limma

0

Pedro López Romero •

**360**wrote: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

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modified 12.0 years ago
by
Naomi Altman •

**6.0k**• written 12.0 years ago by Pedro López Romero •**360**