[Bioc-sig-seq] RNA-seq: test for within sample differential counts

[Michael Dondrup]

Hi,

I need some statistical advise for the following problem. Given an RNA-seq experiment I would like to assess 
statistical significance of differential read-counts >within< a sample. Given a sample with read counts
for two (adjacent) regions out of all all regions of the genome I am interested in, say gene A and intron B. 

I wish to detect if region B has a significantly lower read count than A, lengths of regions A and B are known to be different,
so I think fisher's-exact test does not apply here. Region length should be taken into account for this, as I think that
the more positions are different between regions, the more significant the result should be. I also have biol. replicates,
but these replicates have different numbers of reads. 

Packages like DEseq and edgeR seem to be tailored to between samples comparison. So which method
would you recommend for within sample comparison?

Thank you very much
Michael