[BioC] normalization method & dispersion estimation RNA-seq data

[Ryan C. Thompson]

Anyway, to address the question of using DSS to estimate dispersions and 
then plugging those dispersions into an edgeR DGEList object, this 
should be perfectly possible, with one LARGE caveat: DSS only supports 
the simplest possible experimental design: two-classes, unpaired 
samples. If your experiment fits this design, you can use DSS to 
estimate dispersions and copy those dispersions into a DGEList object 
and use edgeR's significance tests. However, doing so would not 
necessarily be useful because, as discussed, the DSS paper shows that 
doing so would give basically the same results as using the waldTest 
function of DSS.

On 11/26/2012 09:30 AM, aec [guest] wrote:
> Is it possible to adopt the CQN normalization method (Hansen, 2012) as an option of the edgeR function 'calcNormFactors' ? And the new shrinkage estimator for dispersion (Wu, 2012) that seems to be better than the currently used by edgeR ?
>
> thanks,
>
>
>   -- output of sessionInfo():
>
> any
>
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