Background: I had 6 individuals each assigned to either the treatment or control groups (3 per group). I wanted to compare the effect of the treatment and have included the "individual" as a random effect in my mixed model and "treatment" (T or C) as a fixed effects. Issue: I am finding that I get different results based on how I label my replicates (individuals). In the experiment I had the individuals organised as 1,2,3, in the treated group and 4,5,6, in the control group. This was how I was including "individual" in my mixed model originally but I have been since advised that this is incorrect and confounds treatment effects because individuals weren't repeated across treatment and each individual was only assigned one treatment. Instead, I needed to have the nominal values in a repeated structure across treatments (1,2,3 in C and 1,2,3, in T). I get different results depending on how I have the "individual" random replicate effects structured: (T-1,2,3, and C-1,2,3) vs (T-1,2,3 and C-4,5,6,) Question: I dont fully understand why a repeated structure across treatments is correct and I am looking for further clarification.
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