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.
P.S. I originally posted this to Bioconductor Support, but to no avail yet. In order to avoid the loss of information in cross posting, I'll update both posts with the relevant responses, or delete one of the posts (depending on what the mods prefer).