outlier {qpcR}R Documentation

Calculation of qPCR outlier cycles

Description

Calculates the first significant outlier cycle using the studentized residuals method.

Usage

outlier(object, pval = 0.05, nsig = 3)

Arguments

object an object of class 'pcrfit'.
pval the p-value for the outlier test.
nsig the number of successive outlier tests. See 'Details'.

Details

Outliers are calculated essentially as described in the reference below. The steps are:

1) Fitting a linear model to some background cycles 1:x.
2) Calculation of the studentized residuals.
3) Test if the last residual is an outlier in terms of t-distribution.
4) Test if the next nsig - 1 cycles are also outlier cycles.
5) If so, take cycle from 3), otherwise x = x + 1 and start at 1).

Value

A list with the following components:

outl the outlier cycle.
f.outl the fluorescence at outl.

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 <- pcrfit(reps, 1, 2, l5)
out <- outlier(m) 
plot(m)
abline(v = out$outl, col = 2)
abline(h = out$f.outl, col = 2)  

[Package qpcR version 1.2-4 Index]