Adding the clinical framing, because it changes how the question reads. Order of operations matters more than any single choice here: establish a baseline, change one thing, wait long enough for it to express itself, then measure again under the same conditions.

anders_CPH said:

Order of operations matters more than any single choice here: establish a baseline, change one thing, wait long enough for it to express itself, then…

Same pattern here, and in the same order. The detail I would add is minor and it is already implied above.

Moderator note: two posts asking for a source have been merged into one. Please search the thread before asking again. No action needed from anybody.

The figures, for anyone assembling their own picture. The boring version of this is the one that works, and the boring version is: measure a baseline, change one variable, wait, measure again under the same conditions. Nobody wants that answer and it is still the answer.

Following on from anders_CPH — and this may be the naive question:

What would you measure differently if you were starting again?