[BioC] Factorial experiment: No degree of freedom in maanova
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,
>+ 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,
> 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
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives:
Naomi S. Altman 814-865-3791 (voice)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
More information about the Bioconductor