tcell: Microarray Time Series Data for T-Cell Activation

Description Usage Format Source References Examples

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

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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

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# 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)

Example output

Loading required package: corpcor
[1] 100  58
Longitudinal data:
 58 variables measured at 10 different time points
 Total number of measurements per variable: 100 
 Repeated measurements: yes 

 To obtain the measurement design call 'get.time.repeats()'.
[1] TRUE
[1] TRUE
[1] FALSE
$time
 [1]  0  2  4  6  8 18 24 32 48 72

$repeats
 [1] 10 10 10 10 10 10 10 10 10 10

[1] 340  58
Longitudinal data:
 58 variables measured at 10 different time points
 Total number of measurements per variable: 340 
 Repeated measurements: yes 

 To obtain the measurement design call 'get.time.repeats()'.
[1] TRUE
[1] TRUE
[1] FALSE
$time
 [1]  0  2  4  6  8 18 24 32 48 72

$repeats
 [1] 34 34 34 34 34 34 34 34 34 34

[1] "retinoblastoma 1 (including osteosarcoma)"                                                                                             
[2] "cyclin G1"                                                                                                                             
[3] "TNF receptor-associated factor 5"                                                                                                      
[4] "clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"
[5] "mitogen-activated protein kinase 9"                                                                                                    
[6] "CD27-binding (Siva) protein"                                                                                                           
[7] "CD69 antigen (p60, early T-cell activation antigen)"                                                                                   
[8] "zinc finger protein, subfamily 1A, 1 (Ikaros)"                                                                                         
[9] "interleukin 4 receptor"                                                                                                                

longitudinal documentation built on May 2, 2019, 8:23 a.m.