Results are relative expression levels between these two samples only. Each sample must be sent with a control. Comparison of three samples in all pairs requires three arrays. Using Incyte through PittArray. Affymetrix One sample hybridized to each array.
Results are intensity levels normalized to overall background for the chip.
You can also verify this by going back to the software and defining A as the baseline or control chip and comparing C directly. Requires more lab work and expertise. Contact PittArray to find out about costs of hybridization service. Detailed technical information Using Affymetrix through PittArray.