[BioC] 3-way interaction with limma

[Gordon K Smyth]

Hi Elina,

If I understand your aims correctly, I don't think that your contrast is 
quite right.

It's probably helpful to back to first principles here, rather than 
framing the question in terms of interactions.  My understanding is that 
you are interested in differential expression (DE) between mated and 
non-mated females, and in whether this DE depends on the type of male or 
female.  Basically, you are able to compute four possible mating effects:

   Mating.A.C = A.C.yes - A.none.no
   Mating.A.D = A.D.yes - A.none.no
   Mating.B.C = B.C.yes - B.none.no
   Mating.B.D = B.D.yes - A.none.no

I would suggest that you make each of these contrasts and examine then 
individually.  The limma code is almost exactly as above:

cont.matrix <- makeContrasts(
   Mating.A.C = A.C.yes - A.none.no,
   Mating.A.D = A.D.yes - A.none.no,
   Mating.B.C = B.C.yes - B.none.no,
   Mating.B.D = B.D.yes - A.none.no,
levels=design)

You can also make contrasts between any of the mating effects.  For 
example, does the type of the male make any difference for A females?

   A.DvsC = Mating.A.D - Mating.A.C = A.D.yes - A.C.yes

Note that this is not really an interaction.  It is just a comparison 
between two groups, because the non-mated baseline cancels out. 
Similarly, does the type of male make any difference for B females?

   B.DvsC = B.D.yes - B.C.yes

Approached this way, I think you'll find all the contrasts easy to 
interpret.

Best wishes
Gordon

> Date: Tue, 5 Jul 2011 11:12:23 +0100
> From: Elina Immonen <ei10 at st-andrews.ac.uk>
> To: bioconductor at r-project.org
> Subject: [BioC] 3-way interaction with limma
>
> Dear list,
>
> I am trying to pull out a contrast for 3-way interaction using limma, 
> but as I'm pretty new to microarrays I'm puzzling whether I got it right 
> or not. So far I haven't been able to find much info for doing an 
> interaction model involving three factors, so any help is much 
> appreciated.
>
> Here I'm interested in whether the female response to mating depends on 
> female x male type interaction. That is, whether the difference btw. 
> mated and virgin females depends on combination of females and males.
>
> I have 36 one-color Agilent custom arrays with the following nested design:
>
> Factor 1: mating status, levels= yes, no
> Factor 2: female type, levels= A, B
> Factor 3: male type, levels= C, D, none (dummy)
>
> Replication: 6 for each
>
>
> MatingStatus		FemaleType		MaleType
> yes				A				C
> yes				A				D
> no				A				none
> yes				B				C
> yes				B				D
> no				B				none
>
>
>
> Here is my script:
>
> MatingS <- factor(eset$MatingStatus)
> FT <- factor(eset$FemaleType)
> MT <- factor(eset$MaleType)
>
> Mating <- paste (FT, MT, MatingS, sep=".")
> Mating <- factor(Mating, levels=c("A.C.yes",  "A.D.yes", "B.C.yes", "B.D.yes", "A.none.no",  "B.none.no"))
>
> design <- model.matrix(~0+ Mating)
> colnames(design)<-levels(Mating)
>
> fit <- lmFit(eset, design)
>
> cont.matrix <- makeContrasts((A.C.yes-A.none.no)*0.25-(A.D.yes-A.none.no)*0.25-(B.C.yes-B.none.no)*0.25-(B.D.yes-B.none.no)*0.25,
> levels=design)
>
> fit2 <-contrasts.fit(fit, cont.matrix)
> fit2 <- eBayes(fit2)
>
> My questions are:
>
> 1. Is this appropriate way of doing the contrast?
> 2. Why do I get a different number of sig. genes if I swap the order of terms (i.e. bits under parentheses)? In my second approach I've done the contrast in a similar way but with the terms in different orders (all the possible combinations), and then used F test to get a list of genes significant in any of them.
> 3. How do I interpret fold changes from 3-way interaction?
>
> Many thanks for your help.
>
>
> Best,
> Elina
>
>
> ***********************
> Elina Immonen
> School of Biology
> Centre for Evolution, Genes and Genomics
> Dyers Brae House/Sir Harold Mitchell Building
> University of St Andrews
> KY16 9TH, St Andrews, Fife
> Scotland

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