tcell {longitudinal}

Microarray Time Series Data for T-Cell Activation

Description

The data result from two experiments investigating the expression response of human T cells to PMA and ionomicin treatment.

The first data set (tcell.34) contains the temporal expression levels of 58 genes for 10 unequally spaced time points. At each time point there are 34 separate measurements. The second data set (tcell.10) stems from a related experiment considering the same genes and identical time points, and contains 10 further measurements per time point. See Rangel et al. (2004) for more details.

Usage

data(tcell)

Format

tcell.10 and tcell.34 are longitudinal objects, i.e. matrices with 58 colums each and a number of extra attributes (see longitudinal and longitudinal.util).

The vector tcell.gene.descriptions contains the description of the functions of the 58 investigated genes.

Source

This data is described in Rangel et al. (2004).

References

Rangel, C., Angus, J., Ghahramani, Z., Lioumi, M., Sotheran, E., Gaiba, A., Wild, D. L., and Falciani, F. (2004) Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics, 20, 1361–1372.

Examples

# load "longitudinal" library
library("longitudinal")

# load data sets
data(tcell)

# data set with 10 repeats 
dim(tcell.10)
summary(tcell.10)
is.longitudinal(tcell.10)
is.regularly.sampled(tcell.10)
is.equally.spaced(tcell.10)
get.time.repeats(tcell.10)

# data set with 34 repeats 
dim(tcell.34)
summary(tcell.34)
is.longitudinal(tcell.34)
is.regularly.sampled(tcell.34)
is.equally.spaced(tcell.34)
get.time.repeats(tcell.34)

# descriptions of the first nine genes
tcell.gene.description[1:9]

# plot the first nine time series
plot(tcell.10, 1:9)
plot(tcell.34, 1:9)

# Rangel et al. use the combined data set
tcell.44 <- combine.longitudinal(tcell.34, tcell.10)
plot(tcell.44, 1:9)