tcell {GeneTS} | R Documentation |
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.
data(tcell)
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.
This data is described in Rangel et al. (2004) and can be freely
downloaded from
http://public.kgi.edu/~wild/LDS/index.htm. The tcell
object contains the log-transformed and quantile normalized data
(http://public.kgi.edu/~wild/LDS/Bioinformatics_data.xls).
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.
# load GeneTS library library("GeneTS") # load data sets data(tcell) # data set with 10 repeats dim(tcell.10) summary(tcell.10) is.longitudinal(tcell.10) is.regularily.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.regularily.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)