I have an experiment with 4 conditions in it two of them are controls. When I am correcting for batch effects (either with PCA or CCA) should I restrict my comparisons between particular groups? So first I should do control 1 with control 2 then hopefully there will be no DEGs between them. Next I could do Control 2 vs Condition 1 then condition 1 vs condition2 and control 2 vs condtion 2. Sorry if this is confusing but I am trying to avoid going into the experimental details in the interest of keeping this post brief.
As a sort of follow up question can anyone suggest the "standard" or best seurat method for correcting batch effects. I've found some tutorials that recommend using CCA and others suggest PCA.