I'm basically trying to follow up a post I found - https://groups.google.com/forum/#!topic/combat-user-forum/PcTxNlaUmAI
Ultimately, I'm trying to perform a batch correction on Microarray data with two known, and different technical effects (batches).
I realise this can be accounted for using an additive model, but I'm interested on how the ComBat function in SVA could be used to tackle such a problem.
I'm wondering which option is the "done thing":
Apply combat twice - Apply once on Technical effect A, then apply resultant expression set on Technical effect B
Merge All Technical Effects - Regardless of origin, merge Technical Effect A and B into one. i.e, Technical Effect A (two batches; 1 and 2), Technical Effect B (two batches; 1 and 2) - Inform ComBat of 4 Batches.