Five cages have mutant mice. Five cages have normal mice. Each individual mutant cage is paired to one normal cage, because those 6 animals are littermates.

From these mice I take body weights. I then need to test whether significant body weight differences arise due to the mutation with a matched sample t-test.

The question is, does each cage count as an n of 1 or does each animal? TECHNICALLY, I know it is each cage - statistical units need to be independently ramdomised, treated, must not interfere with each other yadda yadda.

But what

*exactly*is it I would need to demonstrate in order to justify using animals as my statistical units? Do I use an ANOVA to show that all the 5 normal cages do not significantly differ, and that all the 5 mutant cages do not significantly differ? Would this show that which cage they were in didn't matter and allow me to use individual animals as my statistical unit? Or do I use an R-squared test to show that the cage that the proportion of variation due to cage is less than some arbitrary amount?

Also, how would I perform matched sample t-test if the analysis was based on individual animals? Just randomly match mutant and normal mice from the paired cages? I guess the mean differences would still be the same regardless of exactly which mice in matched cages were compared eh?