Hi List,
I am having a bit trouble pinning down the interaction terms in DESEQ2. I have followed the user manual, read previous q&a's, and thought I understood. But upon actual application, I realized that I am still confused. 

For simplicity reasons, I will just ask my questions based off the example in user manual 1.5, under section 3.3.


	
		
		
	
	
		
			
				
					



>The main effect of OHT treatment over control for all patients can be extracted with the following:


				
			
			
				
					
						>resOHT <- results(ddsX, contrast = c("treatment","OHT","Control"))

					
				
			
		
	
check.



	
		
		
	
	
		
			
				
					
						>In order to test if the effect for OHT treatment over control is different for patient 4, we test the
interaction term with the folloing:


					
				
			
		
	


	
		
		
	
	
		
			
				
					
						resX <- results(ddsX, contrast =
                list("patient4.treatmentOHT",

						                     "patient4.treatmentControl"))

					
				
			
		
	
1) Point of clarification, effect for OHT treatment over control is different for patient 4 (over all other patients?) As in an ANOVA comparison? These genes are only differentially expressed b/w OHT and control in patient 4?



					
				
			
		
	
2) This is where I am most confused. If there are only 2 levels in the patient variable, patient 4 and patient 5, I'd thought that this would be equivalent to:
contrast=list("patient4.treatmentOHT","patient5.treatmentOHT")
But it's not. So what does the above contrast mean?

3) if we want to do this example with LRT, do we need to fit with a different reduced model depending on what contrast we want to pull out?

Thanks in advance.

-Rob


 		 	   		  
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