I'm newbie to multivariate analysis and working on a project where I'm interested in the strength of association between two pathways (proteomic data). Abstractly speaking, each pathway is represented by a collection of k variables (protein expression levels). For example: pathway A comprises 3 proteins (measured for 100 subjects), and the pathway B comprises 5 proteins (measured for the same subjects). So, I need to compute 'correlation' between two matrices 100x3 and 100x5.
QUESTION How to compute correlation in this case? The naive way is to compute pair-wise correlation and then pool them somehow or via canonical correlation analysis.
Any other ideas?