Chapter 9 Analyze the Comparative CT ExperimentView the Amplification PlotApplied Biosystems 7500/7500 Fast Real-Time PCR System Getting Started Guide for Relative Standard Curveand Comparative CT Experiments166NotesView the Amplification PlotThe Amplification Plot screen displays amplification of all samples in the selected wells.Three plots are available:• ∆Rn vs Cycle – ∆Rn is the magnitude of normalized fluorescence generated by thereporter at each cycle during the PCR amplification. This plot displays ∆Rn as afunction of cycle number. You can use this plot to identify and examine irregularamplification and to view threshold and baseline values for the run.• Rn vs Cycle – Rn is the fluorescence from the reporter dye normalized to thefluorescence from the passive reference. This plot displays Rn as a function of cyclenumber. You can use this plot to identify and examine irregular amplification.• CT vs Well – CT is the PCR cycle number at which the fluorescence meets thethreshold in the amplification plot. This plot displays C T as a function of wellposition. You can use this plot to locate outlying amplification (outliers).Each plot can be displayed as a linear or log10 graph.About theExampleExperimentIn the comparative CT example experiment, you review each target in the AmplificationPlot for:• Correct baseline and threshold values• Outliers
