Lets say I have a design that is ~ drugTreatment + environmentalCondition + drugTreatment:environmentalCondition
with factors with the following levels:
drugTreatment:
- control
- A
- B
environmentalCondition:
- standard
- heat
- osmotic
For the interaction term drugTreatmentA:environmentalConditionheat, one could it interpret its meaning as:
The difference in effect of that drugTreatmentA has when the environment is environmentalConditionheat compared to drugTreatmentAs main effect (on base level environment).
BUT:
I could also interpret the same interaction term as:
The difference in effect of that environmentalConditionheat has when the drug is drugTreatmentA compared to environmentalConditionheats main effect (base level drug).
Is this line of reasoning correct? Intuitivly I feel as if these values could be different.
In terms of design, I guess my question is:
for Design 1: ~ drugTreatment + environmentalCondition + drugTreatment:environmentalCondition
and Design 2: ~ environmentalCondition + drugTreatment + environmentalCondition:drugTreatment
are the interaction terms drugTreatmentA:environmentalConditionheat and environmentalConditionheat:drugTreatmentA the same?
If so, can someone please help me understand why this is the case?
In example 3 of the man page of ?results it makes reference to "the main effect", in my case, I don't know if the environmnet, or the drug is the main effect.
To make my question clearer, I created a diagram, I'd like to understand why the pink and red arrows are the same.

I guess my confusion is coming from my base assumption. Which is that the the two effects on gene expression are not parallel, but rather sequential. For example, If gene 1 is completely silenced in the standard condition, then the drug has no chance of effecting that gene, even if it is a true target. Is it possible for me to figure out the sequential nature of regulation?