guescini2 {qpcR}R Documentation

A qPCR experiment with replicates and simulated inhibition (Lightcycler 480) from Guescini et al

Description

A high quality experiment in which a decreasing amount of PCR mix mimics PCR inhibition.

Usage

data(guescini2)

Format

A data frame with the PCR cycles and 60 qPCR runs from 12 replicates with 5 decreasing steps of PCR mix. The replicates are defined by FX.Y (X = PCR mix dilution number, Y = replicate number). For example:

F1.X 100% Mix
F2.X 90% Mix
F3.X 80% Mix
F4.X 70% Mix
F5.X 60% Mix

Details

The real-time PCR was conducted with primers for the NADH dehydrogenase 1 in a Lightcycler 480 (Roche). The data is background subtracted.

Source

Supplemental data 1 to the paper.

References

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition.
Guescini M et al, BMC Bioinformatics, 2008, 9: 326.

Examples

## Not run: 
### effect of decreasing mix
### on PCR efficiency
data(guescini2)
ml <- modlist(guescini2, fct = l5())
effs <- sapply(ml, function(x) efficiency(x, plot = FALSE)$eff)
### mean for the replicates
tapply(effs, gl(5, 12), function(x) mean(x, na.rm = TRUE)) 
## End(Not run)

[Package qpcR version 1.1-8 Index]