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

[Gordon K Smyth]

Hi Ryan,

edgeR can't.

voom can, but you have to put it together partly yourself.  Just fit voom 
to each timepoint separately, then cbind the voom output objects back 
together.

Or else just proceed in edgeR as if the dispersions are equal across 
timepoints.  This will be conservative but won't give false positive 
results.

Best wishes
Gordon

> Date: Fri, 24 May 2013 12:10:09 -0700
> From: "Ryan C. Thompson" <rct at thompsonclan.org>
> To: bioconductor <Bioconductor at r-project.org>
> Subject: [BioC] Differential expression testing for groups with
> 	unequal	variances/dispersions?
>
> 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

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