Intrasample exon analysis of RNA-Seq data using RPKM values

[desmo]

Hello SeqAns community,

I have been using Mapsplice and RSEM to analyze RNA-Seq data.
The output of my pipeline are the expected counts (or raw count) for genes and isoforms and RPKM values for exons.

What I'm looking for is not an usual differential expression analysis between different sample.

For each gene I want indeed analyze if the first exon is overexpressed in comparison to the last one (so it is an intrasample analysis).
As stated before, each exon has an RPKM value that is a relative abundance units.
But how can I compare this RPKM values? What kind of statistical analysis I sould use to compare these RPKM values?

Any help would be really appreciate.
Thank you!