I have an intervention group (N=1282) and a much smaller control group (N=40) who I have assessed at two different time points (repeated measures). There are 3 dependent variables that I am assessing them on, and these dependent variables are related - Therefore I have decided that MANOVA is a better approach than running three separate ANOVAs.

My understanding is that this will be a mixed MANOVA as I have within subjects (time points) and between subjects (intervention or control group) factors.

My question is, could the differences in the size of the groups (the intervention and the control group) be a problem for this type of analysis? How do I get around this or justify this (it is not possible for me to collect any more control group data unfortunately!)

Your help is greatly appreciated.