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 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- ---------------------------------------------------------------------- ----------------------- 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 [[alternative HTML version deleted]]