I am not statistician so I am sorry if my question formulation sounds confusing.
The ultimate goal is to comapre two methods (A and B). Each method creates 24 numbers (so, 24 pairs). Apart from the method A and B, each of these numbers are linked to the same object. Something like this:
Protein|structure|Method A |Method B MDM2 a1 23 19 MDM2 a2 25 8 MDM2 a3 45 37 P53 b1 19 18 P53 b2 ... ... P53 b3 XXX c1 XXX c2 XXX c3 YYY d1 YYY d2 YYY d3
Ultimate goal is to compare method A to method B and determine whether one method has statistically significant difference to the other.
However, in my case comparison should be considered as pairwise within the Protein (MDM2 for example). So, I should not compare it as
a1A to a1B;
a2A to a2B.... It should more likely be pairwise within a protein:
a1A to a1a2a3B;
a2A to a1a2a3B;
a3A a1a2a3B. Then,
b1A to b1b2b3B.
So ultimately, statistical methods tells me whether method A is statistically different than method B across entire sample. So that, at the end, if I "shuffle" the numbers within each method, but within Protein, I get same result.
Should I just create new, pairwise sample and do simple 2-sample t-test?