Dear Fei,

Thank you for posting this interesting question.

I think that the steps you followed for combining multiple measurements from the same sample are appropriate.

For dealing with different subgroups there might be other options (see, e.g., https://handbook-5-1.cochrane.org/chapte...). For example, you could consider each subgroup as a separate study. I acknowledge that the subgroups have similarities (e.g., because their data were acquired in the same scanner and they share the same controls), but I understand that they also have important differences in clinical or other factors defining the subgroups. You might want to split the sample size of the control group, i.e. 50 vs 25 for one subgroup and 50 vs 25 for the other subgroup.

Hope this helps,

Joaquim