expfit2 {qpcR}R Documentation

Calculation of PCR efficiency by fitting of an exponential model after outlier cycle detection

Description

The outlier cycles (and thus the region when the PCR curve rises significantly above background) are identified by the studentized residual method as in Tichopad et al. (2003). An exponential model is then fit to the next defined number of cycles.

Usage

  expfit2(object, fitcyc = 5, plot = TRUE, pval = 0.01, ...)

Arguments

object a 'drc' object.
fitcyc the number of cycles used for exponential fitting.
plot if TRUE the result is plotted, if FALSE the result is diplayed on the console.
pval the p-value for the outlier significance of the studentized residuals.
... other arguments to be passed to multdrc.

Details

The exponential growth function f(x) = b * exp(d * x) + e is fit to the data. Calls outlier and studres for calculation of the studentized residuals and definition of the outlier cycles. The efficiency is calculated a) from the exponential fit with E = exp(d) (Eff.fit) and b) for each cycle within the exponential region from the raw fluorescence values by E = frac{F(n)}{F(n-1)} (Eff.curve). The inital template fluorescence (F0) is derived from parameter b. If the detection of outlier cycles is problematic (i.e. due to high noise), one can improve results by lowering the p-value.

Value

A list with the following components:

outlier the outlier cycle.
Eff.fit the PCR efficiency calculated from the exponential fit.
Eff.curve the PCR efficiency for each cycle within the exponential phase. See Details.
resVar the residual variance of the fit.
AIC the Akaike Information Criterion of the fit.
RMSE the root-mean-squared-error of the fit.
init the initial template fluorescence, i.e. 'F0'.
mod the exponential model from the best fit.

Author(s)

Andrej-Nikolai Spiess

References

Standardized determination of real-time PCR efficiency from a single reaction set-up. Tichopad et al., Nucleic Acids Research, 2003, e122.

Examples

m <- multdrc(F1.1 ~ Cycles, data = reps, fct = l5())
expfit2(m)

[Package qpcR version 1.0-6 Index]