How are you defining gene/transcript expression?

In [rna-seq.tex](https://github.com/klmr/thesis/blob/master/rna-seq.tex) you have excellent discussion of various aspects of expression quantification. I think there are some missing pieces:
- Given that you state you are interested in transcript quantification, how do you actually quantify transcripts? Mapping to genomic features does not provide this because of shared exons, so how are you getting transcript abundance measures? And how do you handle multi-mapping reads?
- In several places you mention gene expression. How are you defining this? If the molecule of interest is the transcript, how is gene expression defined relative to expression of each transcript?
- RPKM is unstable across samples by definition because the normalisation factor is sample-specific. This is not the case for TPM, which is only unstable due to the molecular population makeup instability that you mention.

Start with rna-seq.tex and review its discussion of expression quantification. Clarify how transcript abundance and multi-mapping reads are handled, define gene expression relative to transcript expression, and correct the RPKM versus TPM explanation; the issue is done when these points are clearly addressed in the thesis.

Written by the indexing model from the issue text.