hi Alicia,

DESeq2 is intended for gene-level analysis. here is some explanation from
Simon on the list as to why doing a count-based analysis at the
transcript/isoform level is problematic:

https://stat.ethz.ch/pipermail/bioconductor/2012-February/043410.html

if you are interested in looking for differential exon usage, you can
instead consider using the DEXSeq package:

publication
http://www.ncbi.nlm.nih.gov/pubmed/22722343

software:
http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

Mike



On Thu, May 8, 2014 at 7:26 PM, Alicia R. Pérez-Porro <
alicia.r.perezporro@gmail.com> wrote:

> Dear Bioconductor users,
>
> I am working with differential expression at the transcript (isoform)
> level. I have 6 different conditions (2 replicates/condition).
>
> I want to know if I can use DESeq2 for that or if the package can only be
> used at the gene level.
>
> Thanks,
> Alicia
>
>
> --
> Alicia R. Pérez-Porro
> PhD candidate
>
> Giribet lab
> Department of Organismic and Evolutionary Biology
> MCZ labs
> Harvard University
> 26 Oxford St, Cambridge MA 02138
> phone: +1 617-496-5308
> fax: +1 617-495-5667
> www.oeb.harvard.edu/faculty/giribet/
>
> Department of Marine Ecology
> Center for Advanced Studies of Blanes (CEAB-CSIC)
> C/Accés Cala St. Francesc 14
> 17300 Blanes, Girona, SPAIN
> phone: +34 972 336 101
> fax: +34 972 337 806
> www.ceab.csic.es
>
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