Can FPKM in different compartment be added directly?

Question

[xidianbill]

Hello, guys. I have a question about RNA-Seq and FPKM. If I seperate the cells into nucleus and cytoplasm, and I use RNA-Seq to sequence the expression level in two cell compartments respectively, can I add the FPKM in two compartments directly to get the FPKM in the whole cell? Or do I need some transformation？

Answer 1

[Devon Ryan]

You would take the weighted average, where the weight is the effective length of the gene in the cytoplasm and the nucleus. If both compartments have the same effective length then this becomes the average of the FPKMs. One doesn't add them, since FPKM is already depth-normalized.