Gene Co-Expression Analysis: Choosing the right Model

Question

[BELA]

Hi all, I am new to the field, but read quite a lot now about Gene Co-Expression/Network Analysis from Microarray Data. Now I find it quite hard to choose the right appraoch to analyze the data and answer my research question.

My design is as follows: - 30 persons Control-Group, 30 persons Trauma-Group - they underwent a stressing test (I am interested in stress-related gene expression) - we have microarray data, 3 time points: -45 mins, +45 mins, +180 mins

Now I have the feeling that WGCNA is a popular tool (and implemented in R), but relatively limited in what I can learn from it. It would be great if I could learn

1. about Co-expression of the Genes (stress-related),
2. about differences between the groups (control, trauma),
3. about time changes in expression during the stress test (3 time points).

I find it soooo hard to decide what method is best suited for my data. I would like to use something implemented in R... Do you have any suggestions?

Thanks for advices!!