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

[Marcelo Laia]

Dear Naomi,

Please, do you suggest me to do a model like 1, 2 or 3?

1. 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, random=~Sample)

2.  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)

3. 1. 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)


The first one is not included in maanova tutorial.

Thank you very much!!!

Marcelo


2008/2/20, Naomi Altman <naomi at stat.psu.edu>:
> I have not used MAANOVA, but I think the problem
>  is probably that you included Sample in your model.
>
>  --Naomi
>
>
>  At 01:03 PM 2/19/2008, Marcelo Laia wrote:
>  >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
>  >
>
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>
>  Naomi S. Altman                                814-865-3791 (voice)
>  Associate Professor
>  Dept. of Statistics                              814-863-7114 (fax)
>  Penn State University                         814-865-1348 (Statistics)
>  University Park, PA 16802-2111
>
>


-- 
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