I have a dataset for proteomics, miRNA, mRNA profiling for three disease groups and controls. I want to see the similarities and differences between networks.
Few suggestions I would need before proceeding-
1. Do i do each dataset separately or out them all together and analyze?
2. Do I run all the phenotypes together?
3. For miRN- do I do the negatively correlated pairs before adding?
You help is much appreciated!