[BioC] Differential expression testing for groups with unequal variances/dispersions?

[Ryan C. Thompson]

Hi all,

I am studying a ChIP-Seq dataset (looking at gene promoter regions in 
human) where it appears that different experimental groups have widely 
different dispersions/variances using edgeR/limma. I have 4 timepoints, 
and if I use edgeR to compute the dispersion for each timepoint 
separately, I get:

0 hours: 0.407
24 hours: 0.505
120 hours: 0.115
2 weeks: 0.0531

So the dispersion seems to range from 0.05 to 0.5. I am looking to test 
for "differential modification" between these timepoints, as well as 
between cell types at each timepoint, etc., and I was wondering if there 
is any differential expression test (or dispersion estimation method?) 
that can handle groups with different dispersions/variances.

For reference, here is my experimenal design as an Excel spreadsheet: 
https://www.dropbox.com/s/3vnk4mai3dh39yv/chipseq-samples.xlsx

And here is the result of plotBCV on each group (look at the last 4 
pages for the time point groups): 
https://www.dropbox.com/s/s4caq1p0h3e4zhm/groupdisps.pdf (Warning: big 
PDF with lots of points which may bring your PDF reader to its knees.)

-Ryan Thompson