What is the difference between gene FPKM and transcript FPKM values? Or rather how is FPKM value for gene obtained from FPKM values of transcript. Average is not suitable as only one transcripts may have expression out of several. So what method is used to do so.
Thak you Seidel for showing the way. I have now been able to find the calculation methods.
The general method for calculation of transcript FPKM is explained here.
As I am using Ballgown tool, I found the answer to my question in supplementary article in one of their papers Ballgown bridges the gap between transcriptome assembly and expression analysis. The gene FPKM vale calulation is explained under the heading Expression data.
It depends on what software you're using, and what you are actually quantifying. Most people gloss over the issue because transcripts and genes are complicated, and specific choices need to be made in order to be precise about either. Nonetheless, generally philosophically speaking: the output of the gene (the gene FPKM) will be considered the sum of the transcript FPKMs. You might read one of the original papers describing how this is done: Trapnell et al., Nature Biotechnology volume 28, pages 511–515 (2010). But of course, there are a variety of ways to estimate these values.