R: Gene expression from real-time quantitative PCR

qpcr {MESS} | R Documentation

## 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.

### 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 <kij@life.ku.dk>.
Added by Claus Ekstrom <ekstrom@life.ku.dk>

### 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))

[Package MESS version 0.5.6 Index]