Dear Bioconductor users, I am working on an invasive plant species and I am trying to analyze a big Nimblegen (1 color) microarray dataset using Rmaanova. Here is my experimental design: 4 Treatments 2 Continents (Europe/America) (Fixed factor), crossed with Treatment 2 Invasive Status (Native and Primary Invasion in Europe, Secondary and Tertiary Invasions in America), nested in each Continent (Fixed factor) 2 Populations nested in each Invasive Status (Random factor) 2, 3 or 4 biological replicates, nested in each Population (Random factor) The number of replicates is not the same in each Population and Treatment because some plants didn't grow. I am mainly interested in: 1) the effect of Treatment 2) the effect of Continent 3) the effect of Invasive Status 4) the interaction between Treatment and Continent 5) the interaction between Treatment and Invasive Status I have a problem with the model contruction (makeModel function in Rmaanova). Apparently, Rmaanova can handle nested designs, but then, how do you code this? I tried the usual way in R (i.e. with %in%): formula=~Treatment + Continent%in%Treatment + Treatment:Continent%in%Treatment + InvasiveStatus%in%Continent%inTreatment + Treatment:InvasiveStatus%in%Continent%in%Treatment I get this error message after calling the makeModel function: Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 91, 0 Any idea of what is going on? Is it a problem with the model formula or something else? Also, if I am not mistaken, Rmaanova cannot deal with interactions between more than two terms, right? If anybody would like to share his/her experience with Rmaanova (things to do or not to do...), that would be greatly appreciated! Thank you very much. Aurélie -- ---------------------------------------------------------------------- -- *Aurélie BONIN* *Postdoctoral Researcher* Department of Biology Indiana University 1001 E. Third Street Bloomington, IN 47405 USA Phone: +1 812-855-9018 Fax: +1 812-855-6705 Email: _abonin@indiana.edu <mailto:abonin@indiana.edu>_ [[alternative HTML version deleted]]