[BioC] technical replicates and spots in limma

[Ron Ophir]

Dear limma experts,
I have direct experiments with two biological replicates and two
technical replicates. In each array sots are printted in 4 replicates.
In duplicateCorrelation help it is written that "At this time it is not
possible to estimate correlations between duplicate spots and between
technical replicates simultaneously."
The question is it possible to average on both technical and spot
replicates but not simultaneously and if yes then how?
If not which least-squares analysis should I drop technical sample
replicates or spots replicates?
Thanks in advance
Ron

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