6.0 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
If all the mice were the same sex, then it would be a 2x2 factorial.
Having both male and female, you have some difficult choices to make,
depending on whether the treatment or the KO can have sex-linked
In the simplest case that the answer is no in both cases, then you
make a design matrix from
design <- model.matrix(~sex+genotype+genotype:treatment)
in order to test for treatment effects within each genotype.
In any case, designing an analysis depends on the questions you want
answer as well as the treatments you have.
> Date: Wed, 2 May 2012 15:34:46 +0100
> From: john herbert <arraystruggles at="" gmail.com="">
> To: <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] Limma analyses;paired and/or factorial design?
> Dear Bioconductors,
> Please can anyone advise on this?
> One colour array; I have 8 mice. Each mouse can have a genotype of
WT or KO.
> For each mouse, there are 2 samples, one with treatment and one
> Is this a combined paired and factorial design and if so, how can I
> construct a design matrix?
> There is also Male and Female (half mice of each group).
> Thank you for any advice on this.
> Kind regards,
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