2009/3/13 Kim Kultima <kim.kultima at="" medsci.uu.se="">: > Dear Marcelo, > > I have read your thread in Biocunductor concering no degree of freedom in > maanova in factorial designs. I have the exact problem you describe in the > tread. In the last thread I see that you solved the problem: > > I already solve that problem. I found that is possible to do the > analysis step-by-step (with interactions and without interactions - > for main effects). > > > Does this mean that you solved the problem by analysing first main effects, > followed by interaction effects, separately? > Is that ok to do? > > Do you know why this problem appear in maanova? > > I hope you have the time to answer my questions. > > Regargs, > > Kim Kultima Dear Kim, Yes, I did the analysis step-by-step and I solved the problem by analyzing first main effects, and after followed by interaction effects. I don't know why this problem appear in maanova. Sorry! May be someone, with more expertise, in the Bioconductor mailing list could be help us in these issues. I hope this help you. Best Regards -- Marcelo Luiz de Laia Jaboticabal - SP - Brazil

2009/3/13 Juan Pedro Steibel <steibelj at="" msu.edu="">: > Hello Marcelo, > I have some experience with MAANOVA and I would be happy to help, but I can > not find the original email in the BIOC list, could you please forward it to > me? > Thanks > Juan P. Steibel Dear Juan, Thank you for your help. Here is the link: https://stat.ethz.ch/pipermail/bioconductor/2008-February/021247.html and all two messages that I receive related on the thread. I'm not currently using maanova, only these two guys. Please, could you help they? I suggest to keep the discussion on list, because it could be useful for someone on the future! Thank you very much! Marcelo 2009/3/11 Goutham Vemuri <goutham at="" chalmers.se="">: Hello Marcelo, I saw the problem that you had with Maanova on the mailing list and I would like to request some help from you on how you solved it. I have the exact problem and I am not able to get the interaction effects. I have 2 strains (Reference and mutant), 2 carbon sources and 2 kinds of nutrient starvation, in duplicate (16 conditions). So, my design file is Array Strain Csource Limit Sample 1 REF GLU C 1 2 REF GLU C 2 3 . . 16 MUT ETH N 2 The model I used was anova.full.mix <- fitmaanova(ciao.raw, formula = ~Strain + Csource + Limitation + Sample + Strain:Csource + Strain:Limitation + CSource:Limitation, random = ~Sample, method = "REML", verbose=TRUE) When I ran the matest as Csource.int.mix <- matest(ciao.raw, anova.full.mix, term="Strain:Csource",n.perm=1,test.method=rep(1,2)) I get the error that there is no DF to do the test. After reading the thread, I could not understand how you fixed the problem to get the interaction effects. Any help is very much appreciated. Thanks. Goutham 2009/3/13 Kim Kultima <kim.kultima at="" medsci.uu.se="">: Dear Marcelo, I have read your thread in Biocunductor concering no degree of freedom in maanova in factorial designs. I have the exact problem you describe in the tread. In the last thread I see that you solved the problem: I already solve that problem. I found that is possible to do the analysis step-by-step (with interactions and without interactions - for main effects). Does this mean that you solved the problem by analysing first main effects, followed by interaction effects, separately? Is that ok to do? Do you know why this problem appear in maanova? I hope you have the time to answer my questions. Regargs, Kim Kultima 2009/3/16 Kim Kultima <kim.kultima at="" medsci.uu.se="">: Dear Marcelo, Thank you for your help. Here is the link: https://stat.ethz.ch/pipermail/bioconductor/2008-February/021247.html I am currently trying to solve the problem by using the nlme library instead. Unfortunaley this library is not at all created for use with microarray data so things has to be re-structured. I have not come up to an solution why it does not work with maanova. I have a three way interaction also, which can not be tested for. I have tried different linear models where it worked, so it should work. I wonder if there is a bug somewhere in the maanova library or similarily. Regards, //Kim