Hello everyone,
I'm working on a scientific project that poses a particular problem. The experimental design includes 3 times and 2 conditions (WT and KO). Each time*condition has 3 mice. In the KO condition, the mice are all female. unfortunately, in the WT condition, at each time point, two mice are female and 1 is male.
The analysis should show the DEGs between the two conditions at each time, but the presence of a male in the WT condition disturbs the result. As there's only one male, I can't just put sex as a covariate in the DEseq2 model because that would risk modelling the individual effect rather than the sexual effect. But I was thinking that as I have 3 males over the 3 times, I could perhaps try to place sex as a random variable taking into account the 3 times and then add the WT vs KO analyses at each time (I want one DEG analysis per time).
However, I'm not sure about the formula in DEseq2. Should it be as follows?
time*condition + (1|sex)
would you have an opinion please ?
Thanks
