Hi Mike,

Thanks for your answer. I read the explanation from Simon and am still a
little bit confuse, reading the edgeR manual I found this: "*edgeR can be
applied to di fferential expression at the gene, exon, transcript or tag
level. In fact, read counts can be summarized by any genomic feature. edgeR
analyses at the exon level are easily extended to detect di fferential
splicing or isoform-specifi c dif ferential **expression*".

So, my initial idea was to treat each isoform like a gene because for the
approach that I am attempting right now I am not interested in differences
in expression of isoforms belonging to the same gene. I did my *de
novo*with Trinity, alignment using Bowtie and estimation of abundance
with RSEM.
I created a matrix with the RSEM counts (isoforms results) and I was
planning on using it as input for my next step.

I understand that even I want to treat each isoform as a gene to do it with
DESeq or DESeq2 is not a good idea. I really don't know about edgeR and am
also considering EBseq.

Suggestions? Thoughts?

Thank you in advance.
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


On Fri, May 9, 2014 at 8:07 AM, Michael Love <michaelisaiahlove@gmail.com>wrote:

> 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
>>
>>         [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>

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