I have not worked with mice data before for paired designs and I could not invest much of thinking before this. For humans its simple we have same subject id and we have multiple measurements or paired design we will go for paired t test etc.
I have an understanding that mice are caged in groups and before today I was using groups comparison and it was easy to do unpaired t test for group-wise comparisons e.g. obese versus control KO for certain gene etc.
However recently, i have to analyze a data where there is this group of 5 mice group caged together. They are on Intermittent fasting food regimen where they are provided food 12 hours a day. two measuremnts are taken at day 1 pre fasting and post feeding. two more measuremants are taken 4 weeks later again pre fasting and post feeding. Together they are 10 measuermnts for say variable X. where X can be any cytokine measurement or glucose or gene expression etc.
Now in order to do a comparison between prefast versus postfed at day 1 and week 4 shall I perform paired t test or unpaired t test and WHy.
My guess is to perform unpaired t test because although the measurement are taken from same mice before and after we don't know which mice is which mice and therefore we cant get the differences of each mice ? which is needed to perform paired t test!
But then there would be violation of assumption of independence which confuses me further because then I can use paired t tets? but how to get the differences of each mouse? Arbitrarily?
I have read about arbitrary pairing sort of thing but i am not able to comprehend the concept fully for lab animals experiments.
Pleas help in explanation why we should do either ?