Example data sets from Vaas et al. (2012)

Description

Two literature example data sets are provided with the opm package, containing one or four plates, respectively.

Format

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.

Details

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.

References

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

Examples

# 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")