
Dear list,
 
I have a 2x3 factorial design and would like to use Limma, however, I have trouble to build the contrast matrix.
 
Here is the 2x3 design
    Treatment:    control, toxinA, toxinB
    Cell line:        wild-type, mutant
 
                       control         toxinA        toxinB
Wild-type          wc               wa            wb
Mutant             mc               ma             mb
 
Question:
    1.  Genes specifically respond to toxinB
    2.  The difference between two cell lines in the toxinB responsive genes.
 
For question A, I used two steps:  1).  genes respond to toxinA:  (wa+ma)-(wc+mc);   2).  genes respond to toxinB:  (wb+mb)-(wc+mc).  Then, I selected genes which respond to toxinB but not respond to toxinA.
 
For question B, I believe that it is interaction question, but how do I set up the contrast?
 
Many thanks in advance.
 
Jason
 
_________________________________________________________________


08
	[[alternative HTML version deleted]]

