Hi,
 
I have 36 Affy grape chips (Vitis Vinifera).
 
Each of the samples has been classified into 4 factors (colour (3
levels), softness (2 levels), parent plant (2 levels), and position (2
levels)). These factors were not introduced experimentally, they were
observed post hoc.
 
There are uneven #'s of samples in each factor, and the factors are not
necessarily independent (esp softness and colour).
 
The question my collaborators are asking is:
Which 1 or more of these 4 factors are important in determining
expression?
 
What is the most elegant way of getting at this? Can limma handle this
situation?
 
Many thanks
 
Tarun Nayar
Genome Sciences Centre
Vancouver BC

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