[BioC] RNAseq object

[Nicolas Delhomme]

Dear René,

Did you look at the vignette by typing in R: vignette("easyRNASeq")? It does explain what the different outputs are and what they can be used for (see section 4.5). Let me know if this is not clear enough in that part of the documentation and I'll try to enhance it. In short, if you want to use edgeR / DESeq, you can just specify these as output. DEXSeq is not supported yet, but is fairly easy to implement (has been on my TODO for a while...). If you want a simple count table (as a matrix m (genes) x n (samples)), then you do not need to precise the outputFormat parameter. If you use the "RNAseq" output, you get the whole object containing the annotation, the counts, etc. And the newly released (or to be soon) version in Bioc 2.11 supports summarizedExperiments that contain the same information. Tim - we are indeed discussing this extensively on the Bioc-devel mailing list and are trying to consolidate the objects used by these different packages. It's on my TODO list to come up with a number of coercion functions, but I'd be glad if you would like to contribute these :-). Finally, we are working on consolidating the different approaches at summarizing reads that exist in at least three different R packages (GenomicRanges, Rsubread, easyRNASeq).

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 1 Oct 2012, at 17:34, Tim Triche, Jr. wrote:

> 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 at 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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