I have questions about how many treatments should be fitted to GLM. Say, I have A, B, C, D 4 treatments, and 1 control, each treatment (including control) has 3 replicates. All treatments and control are the same species. I want to compare A against B and A against control. I am hesitating between two options: first is fit ONLY A, B and control to generlised linear model (GLM) and compare them; second is fit all A, B, C, D and control to GLM, compare any combination of treatment/control pairs, and extract comparisons of A-B and A-control.
Are both reasonable? Which is better? What difference can be expected between the two options?