[BioC] easyRNAseq question

[Nicolas Delhomme]

Dear Nirmala,

I've Cc'ed your email to the Bioconductor mailing list, as it might help other users.

Yes, there is currently a manuscript in review. 

As I'm not sure where you got your information from about the GeneModel summarization, I would direct you to read the new vignette of the development package: http://bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html, page 10 and section 4.6. If that's what you've done or if the information there is not sufficient, let me know and I'll detail it more. By the way, the BestExon summarization did not really prove useful on the datasets I've been working on. I'm thinking about deprecating it.

Best,

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
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On May 24, 2012, at 11:46 PM, Akula, Nirmala (NIH/NIMH) [C] wrote:

> Dear Nicolas,
>  
> Is there a publication that is available for easyRNAseq software? Also, you have mentioned that the transcripts are collapsed to genes by BestExon method and GeneModel summarization. Could you give details on these two methods?
>  
> Thank you very much.
>  
> Best Regards,
> Nirmala
>