[BioC] gage package: biological replicates and technical replicates

[heyi xiao]

I am doing gene set analysis using gage package. I have two sample groups, controls and treated samples. I have one question about using the default 1-on-1 (pairwise) comparison for unpaired samples. My samples have both biological replicates and technical replicates. Shall I treat them the same way? Woud that be a little improper?

Heyi