R: Gene expression data from two-color dye-swap experiment

superroot2 {MESS} | R Documentation

## Gene expression data from two-color dye-swap experiment

### Description

Gene expression levels from two-color dye-swap experiment on 6 microarrays. Arrays 1 and 2 represent the first biological sample (ie, the first dye swap), 3 and 4 the second, and arrays 5 and 6 the third.

### Format

A data frame with 258000 observations on the following 5 variables.

color

  a factor with levels `green` `red` representing the dye used for the gene expression

array

  a factor with levels `1` `2` `3` `4` `5` `6` corresponding to the 6 arrays

gene

  a factor with 21500 levels representing the genes on the arrays

plant

  a factor with levels `rnt` `wt` for the two types of plants: runts and wild type

signal

  a numeric vector with the gene expression level (normalized but not log transformed)

### Source

Data provided by Soren Bak <bak@life.ku.dk>.
Added by Claus Ekstrom <ekstrom@sund.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(superroot2)
    # Select one gene
    g1 <- superroot2[superroot2$gene=="AT2G24000.1",]
    model <- lm(log(signal) ~ plant + color + array, data=g1)
    summary(model)

[Package MESS version 0.5.6 Index]