Experimental setup. Experimental setup used to evaluate the effects of inter-run calibration. On the right side, a sample maximization approach is used to analyze 6 genes for 11 samples in 1.5 run. With gene maximization (left side), IRCs (S1, S2, S3) are required to allow comparison of S5-S7 (run 1) to S8-S11 (run 2 or 3), thus requiring two full runs. The IRCs in run 2 are measured on the same cDNA dilution whereas the IRCs in run 3 are measured on newly prepared cDNA from the same RNA.