[BioC] [MAANOVA] Contrasts for interaction levels - possible?

[Maciej Jończyk]

Dear list members,

I'm analyzing factorial design in MAANOVA pockage.

I wonder is it possible to construct contrast matrix for interaction of
factors.

I have 2x2 factorial design

2 maize lines (dh and dl)
2 temperature treatments (c and k).

I want to get following contrasts:
dhc vs dhk
dlc vs dlk
dhc vs dlc
dhk vs dlk

So I've made contrast matrix (assuming, that ordring of combination of
factors
is: dhc, dhk, dlc, dlk - is it right?):

cont_matx=matrix(c(1,-1,0,0,0,0,1,-1,1,0,-1,0,0,1,0,-1),nrow=4,byrow=T)

And I've got this matrix

> cont_matx
     [,1] [,2] [,3] [,4]
[1,]    1   -1    0    0
[2,]    0    0    1   -1
[3,]    1    0   -1    0
[4,]    0    1    0   -1

But it doesn't work in:


>test=matest(eth_logrg,model.nomainsample,term="linia:temp",Contrast=cont_matx,
n.perm=61,shuffle.method="resid")

Error: The number 1 test is not estimable,

I suppose that problem is with contrast matrix.

I've searched the web a lot of time and find nothing helpful.
So any help will be very appreciated.

Yours sincerely,

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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