kulife (version 0.1-14)

qpcr: Gene expression from real-time quantitative PCR

Description

Gene expression levels from real-time quantitative polymerase chain reaction (qPCR) experiments on two different plant lines. Each line was used for 7 experiments each with 45 cycles.

Usage

data(qpcr)

Format

A data frame with 630 observations on the following 4 variables.

flour	numeric
Fluorescence level	line
factor	Plant lines rnt (mutant) and wt (wildtype)
cycle	numeric
Cycle number for the experiment	transcript
factor	Transcript used for the different runs

Source

Data provided by Kirsten Jorgensen . Added by Claus Ekstrom

References

Morant, M. et al. (2010). Metabolomic, Transcriptional, Hormonal and Signaling Cross-Talk in Superroot2. Molecular Plant. 3, p.192--211.

Examples

data(qpcr)

#
# Analyze a single run for the wt line, transcript 1
#
run1 <- subset(qpcr, transcript==1 & line=="wt")

model <- nls(flour ~ fmax/(1+exp(-(cycle-c)/b))+fb, 
             start=list(c=25, b=1, fmax=100, fb=0), data=run1)

print(model)

plot(run1$cycle, run1$flour, xlab="Cycle", ylab="Fluorescence")
lines(run1$cycle, predict(model))