outlier {qpcR} | R Documentation |
Calculates the first significant outlier cycle using the studentized residuals method.
outlier(object, pval = 0.05, nsig = 3)
object |
an object of class 'pcrfit'. |
pval |
the p-value for the outlier test. |
nsig |
the number of successive outlier tests. See '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).
A list with the following components:
outl |
the outlier cycle. |
f.outl |
the fluorescence at outl . |
Andrej-Nikolai Spiess
Standardized determination of real-time PCR efficiency from a single reaction set-up.
Tichopad et al., Nucleic Acids Research, 2003, e122.
m <- pcrfit(reps, 1, 2, l5) out <- outlier(m) plot(m) abline(v = out$outl, col = 2) abline(h = out$f.outl, col = 2)