ecoli: Microarray Time Series Data for 102 E. Coli Genes Genes

In GeneNet: Modeling and Inferring Gene Networks

Description

This data set describes the temporal expression of 102 genes of E. Coli after induction of the expression of SOD (recombinant human superoxide dismutase).

Usage

data(ecoli)

Format

caulobacter is a longitudinal object containing the data from the Schmidt-Heck et al. (2004) experiment. Essentially, this is a matrix with with 102 columns (=genes) and 9 rows (=time points). All expression levels are given in log2-ratios with respect to the first time point (i.e. the induction at time 0).

Source

The micoarray experiment was performed at the Institute of Applied Microbiology, University of Agricultural Sciences of Vienne. The data and the experiment is described in Schmidt-Heck et al. (2004).

References

Schmidt-Heck, W., Guthke, R., Toepfer, S., Reischer, H., Duerrschmid, K., and Bayer, K. (2004) Reverse engineering of the stress response during expression of a recombinant protein. In: Proceedings of the EUNITE 2004 European Symposium on Intelligent Technologies, Hybrid Systems and their Implementation on Smart Adaptive Systems, June 10-12, 2004, Aachen, Germany, Verlag Mainz, Wissenschaftsverlag, Aachen, 2004, 407-441 (ISBN 3-86130-368-X).

Examples

# load GeneNet library
library("GeneNet")

# load data set
data(ecoli)
is.longitudinal(ecoli)

# how many samples and how many genes?
dim(ecoli)
summary(ecoli)
get.time.repeats(ecoli)

# plot first nine time series
plot(ecoli, 1:9)

Example output

Loading required package: corpcor
Loading required package: longitudinal
Loading required package: fdrtool
[1] TRUE
[1]   9 102
Longitudinal data:
 102 variables measured at 9 different time points
 Total number of measurements per variable: 9 
 Repeated measurements: none 

 To obtain the measurement design call 'get.time.repeats()'.
$time
[1]   0   8  15  22  45  68  90 150 180

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

GeneNet documentation built on Nov. 15, 2021, 1:07 a.m.