Hallo to everyone

I have some questions about interaction term usage:
i have to compare the response to a surgical intervention in heart and 
skeletal muscle


design <- 
cbind(HeartPre=c(1,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0),HeartPost=c(0,1,0,1,0,1,0,1,0,0,0,0,0,0,0,0), 
MusclePre=c(0,0,0,0,0,0,0,0,1,0,1,0,1,0,1,0),MusclePost=c(0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,1))

fit <- lmFit(data.only, design)


Is it better to include interaction term like the following

cont.matrix<-makeContrasts(HeartPost-HeartPre,MusclePost-MusclePre,(MusclePost-MusclePre)-(HeartPost-HeartPre),levels 
= design)

or is it enough to do

cont.matrix<-makeContrasts(HeartPost-HeartPre,MusclePost-MusclePre,levels 
= design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2<-eBayes(fit2)
results <- decideTests(fit2,method="nestedF",p=0.05)        ?

Thank you in advance

Massimo Acquaviva

Department of Molecular Biology
Giannina Gaslini Institute, Genova Italy



Aiutaci ad aiutare: Il tuo 5 per mille a sostegno della RICERCA.
Come fare: nella prossima dichiarazione dei redditi ti chiediamo di 
apporre la firma nel riquadro "Finanziamento agli enti della ricerca 
sanitaria" 
e il codice fiscale dell'Istituto Giannina Gaslini: c.f. 00577500101.
Istituto Giannina Gaslini - www.gaslini.org
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