superroot2: Gene expression data from two-color dye-swap experiment

In kulife: Datasets and functions from the (now non-existing) Faculty of Life Sciences, University of Copenhagen

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.

Usage

data(superroot2)

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 <[e-mail]>.
Added by Claus Ekstrom <[e-mail]>

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)

kulife documentation built on May 2, 2019, 9:53 a.m.