Example data set from Vaas et al. (2012)
OPMS object contains all measurements from
the study by Vaas et al. (2012). Metadata have
been added to fully describe the conducted
phenotype microarray (PM) experiments. The
plate type is ‘Generation III’, but the running
mode was as for the usual PM plates. Four
bacterial strains from two species were considered in the
study. For the three publicly accessible ones, the web
links to their DSMZ catalogue entries are given
OPMS object with the dimensions 114 x 384 x 96, i.e. 114
plates with 384 time points and 96 wells per plate. (10 plates have 364,
365, 368 or 371 time points, respectively; the remaining 74 plates have 384
All plates also contain aggregated and discretised values
from the opm package under default values.
The data set
vaas_et_al is a superset of the data
vaas_1 that come with the
opm package. A particular subset of
vaas_et_al comprising the third technical
repetition in the first experimental run was used for
creating Figure 1 in Vaas et al. (2012). Code for
extracting these plates (and specific wells) is given
below. Please see also the description for the data set
vaas_4 in the opm package for further
details regarding the Figures 2, 3 and 4 in Vaas et
al. (2012). Figure 5 in Vaas et al. (2012)
represents the data for the E. coli strain
DSM 30083T from well
D12 only but comprising all ten technical replicates from
the first experimental run. Finally, the upper part of
Figure 6 shows the data derived only from well C08 in the
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 (http://dx.doi.org/10.1111/j.1462-2920.2012.02719.x).
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://dx.doi.org/10.1371/journal.pone.0034846).
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data(vaas_et_al) plate_type(vaas_et_al) # should indicate generation-III plates (d <- dim(vaas_et_al)) (ha <- has_aggr(vaas_et_al)) (hd <- has_disc(vaas_et_al)) stopifnot(d == c(114, 384, 96), ha, hd) ## Not run: # get the data subset used in Figure 1 in Vaas et al. (2012) vaas.1.3 <- subset(vaas_et_al, query = list(Experiment = "First replicate", 'Plate number' = 3)) # plot the data approximately as in Vaas et al. (2012) xy_plot(vaas.1.3[, , c("D01", "D02", "C10", "C11")], main = "E. coli vs. P. aeruginosa", include = list("Species", "Strain")) level_plot(vaas.1.3[, , c("D01", "D02", "C10", "C11")], main = "E. coli vs. P. aeruginosa", include = list("Species", "Strain")) ## End(Not run)
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