Applied Biosystems discussed this calibration experiment mainly with respect to measuring the absolute amount of a target template in an experimental sample.
A control template (which could be a plasmid clone or the product of
a prior PCR reaction) was carefully quantitated spectrophotometrically.
Samples corresponding to 1250 molecules, 2500 molecules, 5000, 10000,
and 20000 per well were prepared and amplified.
The Ct is plotted versus the log10 of the molecules per well.
The Ct for an experimental sample would be transformed to copies by
reading log CO value from the curve and taking 10^log CO, or solving for
log CO from the slope and intercept of the fit line.
For the purpose of computing a constant for use in calculating relative concentrations, the standard could be in any arbitrary units, because only the slope is used.