One way to assess the assay sensitivity is to monitor the global array metric of percent Present calls. From the same high-quality starting material, the Two-Cycle cDNA Synthesis protocol demonstrates highly comparable P% calls as the results generated from the One-Cycle cDNA Synthesis protocol.

Another way to estimate the detection sensitivity is to use poly-A RNA spike-in controls. Following the recommended protocol included in the GeneChip® Eukaryotic Poly-A RNA Control Kit, the Two-Cycle cDNA Synthesis Kit generally amplifies the samples sufficiently to detect the 3'-Probe Set of lys (the transcript with the lowest concentration, at 1:100,000 complexity ratio) as Present over 70% of the time.