[BioC] Limma: nestedF and interaction term
James W. MacDonald
jmacdon at med.umich.edu
Thu Sep 30 19:54:59 CEST 2010
Hi Massimo,
On 9/30/2010 10:54 AM, MassimoAcquaviva at ospedale-gaslini.ge.it wrote:
> Hallo to everyone,
>
> In have a model like the factorial design example in the limma user
> guide
>
> TS<- factor(TS, levels = c("WT.U", "WT.S", "Mu.U", "Mu.S"))
> design<- model.matrix(~0 + TS)
> colnames(design)<- levels(TS)
> cont.matrix<- makeContrasts(
> WT.SvsU = WT.S - WT.U,
> Mu.SvsU = Mu.S - Mu.U,
> Diff = (Mu.S - Mu.U) - (WT.S - WT.U),levels = design)
> fit<- lmFit(eset, design)
> fit2<- contrasts.fit(fit, cont.matrix)
> fit2<- eBayes(fit2)
>
> I am planning to extract the common response to the treatment between WT
> and Mu using nestedF
>
> cont.matrix<- makeContrasts(
> WT.SvsU = WT.S - WT.U,
> Mu.SvsU = Mu.S - Mu.U)
> fit<- lmFit(eset, design)
> fit2<- contrasts.fit(fit, cont.matrix)
> fit2<- eBayes(fit2)
> results<- decideTests(fit2,method="nestedF",p=0.05)
>
> and to extract the different response testing the interaction term with
> moderated t statistics
>
> cont.matrix<- makeContrasts(
> Diff = (Mu.S - Mu.U) - (WT.S - WT.U),levels = design)
> fit<- lmFit(eset, design)
> fit2<- contrasts.fit(fit, cont.matrix)
> fit2<- eBayes(fit2)
> toptable(fit2,adjust="BH")
>
> and finally make a Venn Diagram with the results of the three comparisons
>
> Is this approach correct to determinate which genes respond only in WT,
> which ones only in Mu and which, among the common ones, are differently
> expressed?
I would tend to keep all comparisons in the contrasts matrix and use
decideTests() to sort out the significantly different contrasts, rather
than splitting the interaction out separately.
Note that this parameterization is different from the classical
parameterization for factorial designs, so there isn't IMO any reason to
preclude all contrasts from being significant simultaneously.
Best,
Jim
>
> I would really appreciate some help
>
> Thank you in advance
>
> Massimo Acquaviva
>
> Department of Molecular Biology
> Giannina Gaslini Institute, Genova Italy
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> 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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>
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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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