Usually 10X the standard deviation of Rn for the early PCR cycles (background activity). The threshold should be set in the region associated with an exponential growth of PCR product (which may be easier in the log-view of the amplification plot is used) and not as high as the linear or plateau sections of the curve. It should be above the highest baseline signal level. It is assigned for each run to calculate the Ct (or Cp) value for each amplification. It may be necessary to have separate different Ct thresholds for each dye used in the reaction.