qpcR (version 1.3-7.1)

Cy0: Cy0 alternative to threshold cycles as in Guescini et al. (2008)

Description

An alternative to the classical crossing point/threshold cycle estimation as described in Guescini et al (2002). A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and the intersection with the x-axis is calculated.

Usage

Cy0(object, plot = FALSE, add = FALSE, ...)

Arguments

object

a fitted object of class 'pcrfit'.

plot

if TRUE, displays a plot of Cy0.

add

if TRUE, a plot is added to any other existing plot, i.e. as from plot.pcrfit.

...

other parameters to be passed to plot.pcrfit or points.

Value

• The Cy0 value.

Details

The function calculates the first derivative maximum (cpD1) of the curve and the slope and fluorescence $F_{cpD2}$ at that point. Cy0 is then calculated by $Cy0 = cpD1 - \frac{F_{cpD2}}{slope}$.

References

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. Guescini M, Sisti D, Rocchi MB, Stocchi L & Stocchi V. BMC Bioinformatics (2008), 9: 326.

Examples

## single curve with plot
m1 <- pcrfit(reps, 1, 2, l5)
Cy0(m1, plot = TRUE)

## add to 'efficiency' plot
efficiency(m1)
Cy0(m1, add = TRUE)

## compare s.d. of replicates between
## Cy0 and cpD2 method. cpD2 wins!
ml1 <- modlist(reps, model = l4)
cy0 <- sapply(ml1, function(x) Cy0(x))
cpd2 <- sapply(ml1, function(x) efficiency(x, plot = FALSE)$cpD2)
tapply(cy0, gl(7, 4), function(x) sd(x))
tapply(cpd2, gl(7, 4), function(x) sd(x))