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

Naomi Altman naomi at stat.psu.edu
Wed Feb 20 16:00:35 CET 2008

I have not used MAANOVA, but I think the problem 
is probably that you included Sample in your model.


At 01:03 PM 2/19/2008, Marcelo Laia wrote:
>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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>Bioconductor at stat.math.ethz.ch
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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

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