Hi!

I am aware of an old post at biostars: In Which Order Use Normalization And Batch Effects Removal? https://www.biostars.org/p/83531/

I think many visitors to this BioC forum perform these procedures routinely. I need a general advice on the order of these procedures in microarray analysis.

Thanks.

I'd normalise first to remove your technical variation within batches, if this was RNA-seq then some samples might have way more reads in than others and that would need correcting for. Then batch is like differences between certain labs and operators etc, so that can be done afterwards.