I'm interested in making a co-expression network out of RNA-seq data that I have for 3 different samples (developmental stages) without replicates. Is there a minimum no. of samples needed to make informative co-expression networks? or is 3 good enough? Are there any good programs that anyone can recommend?
Thanks a lot!!!
What is your definition for co-expression network. What are the nodes in your network and what are the conditions for connecting two nodes?
The nodes would be genes and the condition for connecting the nodes would be if they have similar expression profiles across the 3 developmental stages. If they are similar they should form a module and it could be speculated that these are co-regulated.