R: Microarray Time Series Data for 102 E. Coli Genes Genes
ecoli
R Documentation
Microarray Time Series Data for 102 E. Coli Genes
Genes
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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GeneNet)
Loading required package: corpcor
Loading required package: longitudinal
Loading required package: fdrtool
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GeneNet/ecoli.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ecoli
> ### Title: Microarray Time Series Data for 102 E. Coli Genes Genes
> ### Aliases: ecoli
> ### Keywords: datasets
>
> ### ** Examples
>
> # load GeneNet library
> library("GeneNet")
>
> # load data set
> data(ecoli)
> is.longitudinal(ecoli)
[1] TRUE
>
> # how many samples and how many genes?
> dim(ecoli)
[1] 9 102
> summary(ecoli)
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()'.
> get.time.repeats(ecoli)
$time
[1] 0 8 15 22 45 68 90 150 180
$repeats
[1] 1 1 1 1 1 1 1 1 1
>
> # plot first nine time series
> plot(ecoli, 1:9)
>
>
>
>
>
> dev.off()
null device
1
>