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 . [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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 . [[alternative HTML version deleted]]