[BioC] LIMMA-interaction term

James W. MacDonald jmacdon at med.umich.edu
Mon Oct 4 17:13:36 CEST 2010


Hi Massimo,

On 10/4/2010 4:04 AM, MassimoAcquaviva at ospedale-gaslini.ge.it wrote:
> 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)

If you are interested in the interaction, then you have to explicitly 
include that term in your contrasts matrix.

Best,

Jim


>
> 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
> .
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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