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:

1. 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.
2. 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?
3. There are biological replicates also, each replicate has a specific FPKM value under each treatment. How do I treat these replicates?

Thanks
Dear Ashish,

For your situation, I would not use MeV.

I recommend reading your data into R and then transforming to Z scale via *zFPKM*. You may then use standard statistical tests on these Z-scores for the purpose of identifying statistically significant genes.

You may take a look at this thread where I give some information on producing heatmaps in R: https://www.biostars.org/p/274509/

Also, here is a more advanced version of a heatmap in R: https://www.biostars.org/p/273155/

Kevin
