Thank you very much for your reply!

I have one more question: if I proceed including the interaction term in 
the analysis 

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

should I consider only probe sets found  significant also in interaction 
as truly differentially expressed genes among the two tissues?
And for probe sets found significant only in the overlap between the two 
main effects comparisons (DEGs in common) but not in the interaction term 
is it correct to avarage their logFCs?

I am sorry for my twisted questions

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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