I'm using multiple previously published RNA-Seq studies as validation and to search for similar "signatures" as in our data. For these other studies I have their final read counts, and statistically significant filtered data that includes RPKM, FPKM, or other normalized read values as per their publications.
My question is that I used a cut-off of RPKM > 1 and FPKM > 1 to say whether or not a gene is expressed in the respective study. A reviewer has now responded that this is not informative and the cut-off is too low. In at least two of the studies they used this same cutoff to say whether or not a gene is expressed. I'm wondering what is a more appropriate cut-off to claim whether or not a gene is expressed? Should it be then higher RPKM cutoff and say >= 10 reads per gene (???).
My supervisors are of no help in this and I don't have help in my lab regarding this. :(