If edgeR and/or DE[X]Seq can't take a SummarizedExperiment as input, I will
write a coercion function so that they can.  Let me know if this is an
issue.

Any thoughts from the authors of said packages?  Personally I'd like to see
all of the RNAseq packages on a level playing field, and feel that Nico has
made some tremendous strides in usability, but that's just my opinion (,
maaaan).

Personally I'm only interested in differential isoform usage (in terms of
precision RNAseq modeling) but SummarizedExperiments are a great structure.


On Mon, Oct 1, 2012 at 6:36 AM, René Böttcher [guest] <
guest@bioconductor.org> wrote:

>
> Dear all,
>
> I am a new user of easyRNASeq and would hence like to know which
> advantages the RNAseq output format offers. My intention is to use edgeR
> and/or DESeq afterwards, so I need  the corresponding objects for further
> analysis. Can these be derived from the RNAseq object or do I need to rerun
> the easyRNASeq function with adjusted parameters? I am sorry if this is a
> trivial question but I could not find an answer in the manual.
>
> Kind regards
>
>  -- output of sessionInfo():
>
> -
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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