[BioC] Limma analyses;paired and/or factorial design?

[Gordon K Smyth]

Dear John,

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 effects. 
In the simplest case that the answer is no in both cases, then you might 
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 to 
answer as well as the treatments you have.

Best wishes
Gordon

> 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 control.
>
> 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,
>
> John.

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