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>_


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