I have 4 induced and 4 control samples (technical replicates). I ran cuffdiff to find differentially expressed genes. Now I want to create Heat Map, showing differentially expressed genes across each replicates (not condition) using Log fold change values. Is there any method to extract FPKM values for each replicate and calculate Log fold change? Or would it be appropriate to use EdgeR to perform pairwise comparison (induced1 vs control1 , induced1 vs control2 ....) between each replicate to get the log fold changes for the genes?
Note: I tried treating each replicate as a sample in cuffdiff but this method reduced the power of detecting differentially expressed genes because of the low coverage for replicates.