[BioC] limma 3-way interaction

[Jake]

Okay I think I get it now.  I couldn't figure out what the "assign" part
was for.  It refers to the term in the expanded formula which led to the
term(s) you're interested in, for example:

a*b -> Y = int + a + b + ab
	    0    1   2   3

hence the line

cont.ia <- diag(p)[,attr(X,"assign")==3]

so for a three-way interaction it would be:

a*b*c -> Y = int + a + b + c + ab + ac + bc + abc
	      0    1   2   3   4    5    6    7 

so the line would change to 

cont.ia <- diag(p)[,attr(X,"assign")==7]


Am I interpreting this right?  

--Jake

On Thu, 2006-05-18 at 09:22 -0600, Jake wrote:
> Hi all,
> 
> A while back I found some great code on the list to test for a two-way
> interaction in limma:
> 
> > If you only want F-tests for interactions, the following code would
> work:
> >
> > X <- model.matrix(~a*b)
> > fit <- lmFit(eset, X)
> > p <- ncol(X)
> > cont.ia <- diag(p)[,attr(X,"assign")==3]
> > fit.ia <- eBayes(contrasts.fit(fit, cont.ia))
> >
> > Now fit.ia contains the F-statistic and p-values for the interaction
> in
> > fit.ia$F and fit.ia$F.p.value.
> >
> 
> This code has worked very well for me.  I hand-coded an interaction
> using contrasts and got the exact same results as with using the above
> code - which was encouraging.
> 
> How could this code be adapted for a three-way interaction, ie:
> 
> X=model.matrix(~a*b*c)
> 
> Is it safe to just to substitute this line?
> 
> Any help much appreciated!
> 
> --Jake
> 
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