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

[Naomi Altman]

If each mouse receives both treatments, this is a split plot design 
with genotype:gender as the whole plot factor and treatment as the 
subplot treatment.  You need to have a block effect for mouse.  Since 
these are 1 color arrays, you can simply put in mouse as block.

--Naomi

At 08:00 PM 5/3/2012, Gordon K Smyth wrote:
>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.
>
>______________________________________________________________________
>The information in this email is confidential and inten...{{dropped:11}}