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 > >"Voc? v? as coisas como elas s?o e pergunta: por qu?? Mas eu sonho com >coisas que nunca foram e pergunto: por que n?o? " - Bernard Shaw > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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

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 > > > >"Voc? v? as coisas como elas s?o e pergunta: por qu?? Mas eu sonho com > >coisas que nunca foram e pergunto: por que n?o? " - Bernard Shaw > > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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 "Voc? v? as coisas como elas s?o e pergunta: por qu?? Mas eu sonho com coisas que nunca foram e pergunto: por que n?o? " - Bernard Shaw