I have FPKM values for a number of genes. I want to make a heatmap and find differentialy expressed genes. Here I have three questions:
- Should I use FPKM values directly to make a heatmap or is there anything which has to be done to FPKM values before using them to make a heatmap? I am using MeV to make a heatmap.
- How do I find differentially expressed genes here? I read that taking log2 values of FPKM and then setting the cutoff as 2 will give differentially expressed gene. Taking the cutoff as 2 sounds very arbitrary, is there any reason to take 2 as the cutoff?
- There are biological replicates also, each replicate has a specific FPKM value under each treatment. How do I treat these replicates?