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

[john herbert]

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.