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

[Zhijin Wu]

For normalization with CQN, Kasper (CQN maintainer) has example code how 
to import the offset into edgeR 
(http://www.bioconductor.org/packages/release/bioc/vignettes/cqn/inst/doc/cqn.pdf). 


The new shrinkage estimate provided by DSS can also be used to replace 
the estimate edgeR and Hao Wu (the author of the DSS pacakge) will add 
the example code to the vignette (soon hopefully, when he gets back from 
vacation).

Whether these two will be included as options of functions within edgeR 
can only be determined by the edgeR maintainers (Mark, Davis, Yunshun 
and Gordon)

Jean Wu
On 11/26/2012 12:30 PM, 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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