As I understand it, you can not use duplicate spots and technical 
replicate (dye swap in this instance) together.

So I was wondering how people would approach this data.

3 sets of dye swaps. Each array has duplicate spots.

If I treat the dye swaps as biological replicates, this would be using all 
the data, but the p-values would not be accurate, since they rely on the 
experiments being biological replicates.

I could just use 1 experiment from each dye swap.

I could use all 6 experiments but use one spot for each experiment.

Any thoughts or suggestions?

Lance Palmer
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