vaas_4 {opm} | R Documentation |
Two literature example data sets are provided with the opm package, containing one or four plates, respectively.
vaas_4
is an OPMS
object with the dimensions 4 x
384 x 96, i.e. 4 plates with 384 time points and 96 wells per plate.
vaas_1
is an OPMD
object with the dimensions 384 x 96,
i.e. a single plate with 384 time points and 96 wells.
The OPMS
object vaas_4
contains
measurements from four selected plates from the study by
Vaas et al. (2012). Metadata have been added to
fully describe the conducted PM experiments:
these plates are the sixth technical replicate from the
first biological replicate for the four bacterial strains
considered in the study.
This particular subset served as input for Figure 2 in
Vaas et al. (2012), which can be reproduced by
running xy_plot
with vaas_4
.
Accordingly, Figure 3 in Vaas et al. (2012)
represents the wells G11 and H11 selected from
vaas_4
. Figure 4 focuses then further on that
subset, namely showing the data from strain DSM
30083T (left curve) and strain
Pseudomonas aeruginosa DSM 1707 (right
curve).
The OPMD
object vaas_1
contains
measurements from a single selected plate from the study
by Vaas et al. (2012). Metadata have been added to
fully describe the conducted PM experiments:
this plate is the sixth technical replicate from the
first biological replicate for the strain
Escherichia coli DSM
30083T (yes, the type strain
of E. coli). This is a subset of vaas_4
.
The complete data set is available as vaas_et_al
in the opmdata package.
Bochner, B.R., Savageau, M.A. 1977. Generalized indicator plate for genetic, metabolic, and taxonomic studies with microorganisms. Applied and Environmental Microbiology 33, 434–444.
Selezska, K., Kazmierczak, M., Muesken, M., Garbe, J., Schobert, M., Haeussler, S., Wiehlmann, L., Rohde, C., Sikorski, J. 2012 Pseudomonas aeruginosa population structure revisited under environmental focus: impact of water quality and phage pressure. Environmental Microbiology 14, 1952–1967.
Vaas, L. A. I., Sikorski, J., Michael, V., Goeker, M., Klenk H.-P. 2012 Visualization and curve parameter estimation strategies for efficient exploration of Phenotype Microarray kinetics. PLoS ONE 7, e34846.
http://www.dsmz.de/catalogues/details/culture/DSM-1707.html
http://www.dsmz.de/catalogues/details/culture/DSM-18039.html
http://www.dsmz.de/catalogues/details/culture/DSM-30083.html
# This yields a variable 'vaas_4' containing the data.
data(vaas_4, package = "opm")
# This yields a variable 'vaas_1' containing the data.
data(vaas_1, package = "opm")