I am assigning 384 samples to four 96-well plates for a gene expression analysis. Samples are pairs before and after treatment with one of two drugs. I need to randomize the covariates among the plates to avoid batch effects confounding experimental variables: sample sex, pre-treated vs post-treated in the same sample, and the four different drugs. The simplest method I can think of is to assign plates randomly:
plate = sample( rep( c(1,2,3,4),96 ) )
I can check the assignments after the fact to ensure there are roughly equal distributions of each covariate across the plates with
Is there any compelling reason to do this any other way?
EDIT: More details on covariates:
Time: each mouse was sampled twice, pre- and post-treatment. Sex: Our assay is modestly influenced by sex. Treatment: Each mouse got one of four treatments (Two drugs, two vehicle controls)
Mice are from a genetically heterogeneous cross so they are not inbred littermates, but for the purposes of the experimental design all mice within a treatment are biological replicates.