[BioC] DeSeq - How to get the Biological Coefficient of Variation

[Simon Anders]

Hi Miguel

On 04/12/2012 05:23 PM, Miguel Gallach wrote:
> I got the biological coefficient of variation (BCV) with edgeR by
> calcualting sqrt(tagwisedisp).
> I'd would like to compare it with the BCV given by DeSeq. However I am not
> sure what variable in DeSeq gives me the equivalent value for comparison.
> Should I use the sqrt(perGeneDispEsts) or the sqrt(fittedDispEsts) function
> provided by the fitInfo function?... or maybe none of them?
>
> My naive expectation is that I should obtain with DeSeq very similar BCV
> values for each gene to those obtained with edgeR, right?

I would expect that the tagwise dispersion value provided by edgeR is 
typically somewhere in between DESeq's fitted dispersion estimate and 
the per-gene dispersion estimate.

Early versions of DESeq only used the fitted dispersion value, which was 
unsatisfactory because it made DESeq rather vulnerable to outliers. This 
is why we now perform the quite conservative approach of using the 
maximum of these to values. See this post for details: 
https://stat.ethz.ch/pipermail/bioconductor/2011-December/042441.html

EdgeR instead uses shrinkage estimation to find a compromise between 
these extremes. In principle, this is preferable to our more naive 
approach as it offers more power, and you may wonder why DESeq does not 
use something similar. The reason is that we feel that edgeR's specific 
shrinkage estimator does not offer the robustness we consider required 
(at least in our simulation) and hence opted for DESeq's current simple 
but safe approach, while we are thinking about something better.

The bottom line is: The true value is somewhere between the two values 
that DESeq gives you. EdgeR attempts to find this middle ground, DESeq 
does not, and the reason for this difference is that the edgeR authors 
and we disagree on whether existing schemes to do so are reliable for 
the kind of data that users may apply them to in practice. As you are 
already comparing both tools, you will probably form your own opinion.

   Simon