I have two bacterial strains - one is wild type and the other has one gene deleted. In my experiment, I calculate some observable characteristic (which is continuous) for both of these strains. I repeat this experiment 5 times. Now I want to see if there is a difference between the two strains, so I perform a t-test (assuming the data is normally distributed for now). My question is - should I perform a paired t-test or unpaired? I am a bit confused about it since I feel I have some rationale for doing it either ways -
Why I think its paired : in every replicate, I compare the same two strains and I repeat this 5 times
Why I think its unpaired : Its not like I am subjecting the same strain to two different conditions (which often happens in paired tests). Rather, I have two different strains being subjected to the same condition.
Any help would be appreciated!
Cross posted at Biostars.org