[BioC] Testing for differential expression variability with edgeR

[Gordon K Smyth]

Dear Miguel,

Well, you could obviously subset your data, and compute the tagwise 
dispersions separately for each subset, and compare the two.  Do a formal 
test requires a more work, and would be genewise anyway.

I find it hard to imagine in what context it would make sense to test 
whether two libraries (R4.Hot and R5.Hot) are more different than two 
other libraries.  For a particular gene?  Averaged over genes?

Could you not just make an MDS plot and look to see how far apart the 
samples are from each other?

What are you trying to achieve here from a biological point of view?  What 
biological question are you trying to answer?

Best wishes
Gordon

> Date: Tue, 21 Feb 2012 15:16:53 +0100
> From: Miguel Gallach <miguel.gallach at univie.ac.at>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] Testing for differential expression variability with
> 	edgeR
>
> Dear Bioconductor list,
>
> I am using edgeR to test for differential expression but I also I would
> like to know how to test whether expression variability (per gene) is
> significantly different between biological groups or treatments.
>
> For instance, the next is my experimental design, according to which I have
> two treatments (Hot and Cold) and two biological groups (Hot Adapted and
> Cold adapted; two replicates each).
>
> $samples
>                 group lib.size norm.factors
> R4.Hot     HotAdaptedHot 17409289    0.9881635
> R5.Hot     HotAdaptedHot 17642552    1.0818144
> R9.Hot    ColdAdaptedHot 20010974    0.8621807
> R10.Hot   ColdAdaptedHot 14064143    0.8932791
> R4.Cold   HotAdaptedCold 11968317    1.0061084
> R5.Cold   HotAdaptedCold 11072832    1.0523857
> R9.Cold  ColdAdaptedCold 22386103    1.0520949
> R10.Cold ColdAdaptedCold 17408532    1.0903311
>
>
> I would like to detect those genes for which the expression variability
> between R4.Hot and R5.Hot is significantly different to that obtained for
> R4.Cold and R5.Cold. Can I use the tagwise dispersion values provided by
> edgeR, and how??
>
> Many thanks!
> Miguel
>

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