Hi Simon,

Thanks for the quick reply. A GLM taking into account main or interaction
effects is really what I want. I was thinking on sequencing 10 animals. So
as I have 2 breeds, 2 tissue types and 2 diets, I will have a total of 4
libraries with 10 biological replicates each. The phenotype between breeds
and tissue type is very different and I was hoping that at least within the
subset of a tissue type I could discriminate between the genetic background
(breed) and environmental (diet). You think this is not enough?

Thanks

Kind regards,

Andreia

On Mon, Apr 9, 2012 at 12:21 PM, Simon Anders <anders@embl.de> wrote:

> Hi Andreia
>
>
> On 2012-04-09 13:06, Andreia Fonseca wrote:
>
>  I am planning an experiment to profile miRNAs by ngs with the following
>> multifactorial design: breed, tissue type, diet, tissue color. Is it
>> possible with DEXSeq to account with the effect of interaction between
>> these factors?
>>
>
> Sure, however you want to use DESeq, not DEXSeq. The latter is to test for
> differential exon usage, and as there is no alternative splicing of miRNAs,
> this is not what you want. DESeq allows you to fit a GLM on expression
> levels and test for main or interaction effects.
>
> By the way, I hope you realize that a design with so many factors is
> challenging and requires a large number of samples, especially given that
> you will have to cope with differences in genetic background within breed,
> which will be hard to control for. Assuming you are talking about mammals,
> I would be rather surprised if it turned out possible to get enough power
> to detect interactions without a sample number going into the hundreds.
>
>  Simon
>
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-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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