|Qlucore Omics Explorer supports analysis of dye-swapped two-color loop designs.|
You should do the following:
Each channel from each array should be handled as a separate sample.
Take logarithms of the data if needed. (This can be done either before or after loading the data in Qlucore Omics Explorer.)
Add "Array" as an eliminated variable.
If the two dyes have different affinity for DNA, also add "Dye" as an eliminated variable.
See the reference manual for more information on experiment designs and the use of eliminated factors.