Dear list,
My question may be quite basic and it concerns the rma algorithm for affy data. As the idea behind rma is to take into account the between array variance for a probe set to calculate an expression value, I'm not sure if I can run rma on a set of cel files representing different conditions - for example  have 2 conditions, each replicated 3 times - 6 arrays total. should rma be run for all 6 arrays or for each of three separately. in extreme I may have non-replicated experiments - use rma or not?
Any suggestions are greatly appreciated!
Thanks
Max

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