PrimEff {MCMC.qpcr}

Determines qPCR amplification efficiencies from dilution series

Description

Runs linear regression on Cq versus log2(RNA concentration), plots graph, reports slope (ideally should be -1), and efficiency (with 95 percent credible limits)

Usage

PrimEff(data, plot = TRUE)

Arguments

data

a dataframe containing three columns. First is RNA concentration. This could be absolute as well as relative concentration (1/dilution factor). Second is the Cq value. Third is gene name. Replicate the same name across all the corresponding RNA concentrations. The dataframe may contain data for multiple genes.

plot

set plot=FALSE if the plot is not required

Details

Run with at least 8 2-fold dilutions per gene

Value

Plots the regression and under it, the values of slope and efficiency (plus and minus one SD). The dataframe may contain data for multiple genes, which will all be plotted together (so the reasonable limit is something like 25 genes)

Also returns a dataframe with columns: gene, efficiency, plus one SD, minus one SD, and intercept.

Author(s)

Mikhail V. Matz, UT Austin <[e-mail]>

References

Matz MV, Wright RM, Scott JG (2013) No Control Genes Required: Bayesian Analysis of qRT-PCR Data. PLoS ONE 8(8): e71448. doi:10.1371/journal.pone.0071448

Examples

data(dilutions)
PrimEff(dilutions)