Question: multifactorial analysis
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gravatar for Andreia Fonseca
7.7 years ago by
Andreia Fonseca810 wrote:
Hello, 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? Thanks. Andreia ---------------------------------------------------------------------- ------------------------- 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]]
dexseq • 679 views
ADD COMMENTlink modified 7.7 years ago by Gordon Smyth39k • written 7.7 years ago by Andreia Fonseca810
Answer: multifactorial analysis
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gravatar for Simon Anders
7.7 years ago by
Simon Anders3.6k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.6k 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
ADD COMMENTlink written 7.7 years ago by Simon Anders3.6k
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]]
ADD REPLYlink written 7.7 years ago by Andreia Fonseca810
Answer: multifactorial analysis
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gravatar for Gordon Smyth
7.7 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:
Dear Andreia, See McCarthy et al, Differential expression analysis of multifactor RNA- Seq experiments with respect to biological variation. Nucleic Acids Research, 28 January 2012. http://nar.oxfordjournals.org/content/early/2012/02/06/nar.gks042 Best wishes Gordon > Date: Mon, 9 Apr 2012 12:06:46 +0100 > From: Andreia Fonseca <andreia.fonseca at="" gmail.com=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch="">, <sanders at="" fs.tum.de=""> > Subject: [BioC] multifactorial analysis > > Hello, > > 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? > Thanks. > > Andreia > > -------------------------------------------------------------------- --------------------------- > 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 at fm.ul.pt ; andreiaamaral at fc.ul.pt ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 7.7 years ago by Gordon Smyth39k
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