qpcR (version 1.2-2)

guescini2: 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

source

Supplemental data 1 to the paper.

Details

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

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

## effect of decreasing mix
## on PCR efficiency
data(guescini2)
ml <- modlist(guescini2, model = l4)
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))