sliwin: Calculation of PCR efficiency by the window-of-linearity method
Description
A linear model is fit to a sliding window of the logarithmized raw fluorescence and the regression coefficient is calculated.
At the point of maximum regression (log-linear range), the PCR efficiency is calculated.
the -/+ border from the second derivative maximum cycle in which to do the fitting procedure.
plot
if TRUE the result is plotted, if FALSE the result is diplayed on the console.
Value
A list with the following components:
effthe (maximal) PCR efficiency found within the sliding window.
rmaxthe maximum R-squared.
initthe initial template fluorescence F0.
Details
To avoid fits with a high R-squared in the baseline region, the second derivative maximum is taken as a fixpoint.
This value is consequently always near to the exponential region of the data and avoids the problem above.
The efficiency is calculated by $E = exp(slope)$, as the transformed raw data was based on the natural logarithm.
The initial template fluorescence (F0) is thus calculated by $F0 = exp(intercept)$.
References
Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data.
Ramakers C et al., Neuroscience Letters, 2003, 339, 62-66.