[BioC] Factorial experiment: No degree of freedom in maanova

[Marcelo Laia]

Hi,

We have a factorial experiment like this:

2 Varieties (resistant and susceptible)
2 Conditions (with inductor and with H2O)
2 Treatments (inoculated and non inoculated)
4 Times points
3 biological repetitions
96 arrays (one color)

We start to run the analysis on maanova package.

In our design file design.txt there are these columns:

Array	Dye	Var	ind	Trat	Time	Sample
1	1	Res	H2O	Inoc	6h	1
(...)
96	1	Susc	Ind	N_inoc	48h	3

We had been adjusted these model:

anova.full.mix <- fitmaanova(data=leonardo.raw.averaged,
+ formula=~Var+ind+Trat+Time+Var:ind+Var:Trat+Var:Time+
+ ind:Trat+ind:Time+Trat:Time+Sample, random=~Sample)

When we try to run the matest function,

ftest.full.Var.mix = matest(leonardo.raw.averaged,anova.full.mix,
+ term="Var",n.perm=100,test.method=rep(1,3))

 we got a "No degree of freedom" error.

We only could do that if we remove the interactions from the formula
in fitmaanova function!

But, we like to get the interactions results.

Are we doing anything wrong or is it impossible to fit a model to got
the interactions?

There are another way to got these interactions in our experiments?

In try to insert Array in the formula (random), but the problem continues.

Could you help?

Is possible to got interactions results in our experiments?

Any comments is very appreciated!

Thank you very much

-- 
Marcelo Luiz de Laia
Jaboticabal - SP - Brazil

"Você vê as coisas como elas são e pergunta: por quê? Mas eu sonho com
coisas que nunca foram e pergunto: por que não? " - Bernard Shaw