Example data set from Vaas et al. (2012)

Description

This OPMS object contains all measurements from the study by Vaas et al. (2012). Metadata have been added to fully describe the conducted OmniLog(R) 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 below.

Format

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 time points).

Details

All plates also contain aggregated and discretised values generated via do_aggr and do_disc from the opm package under default values.

The data set vaas_et_al is a superset of the data sets vaas_4 and 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 time-series experiment.

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 (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).

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

data(vaas_et_al)
plate_type(vaas_et_al) # should indicate generation-III plates

## [1] "Gen III"

(d <- dim(vaas_et_al))

## [1] 114 384  96

(ha <- has_aggr(vaas_et_al))

##   [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [29] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [43] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [57] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [71] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [85] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [99] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [113] TRUE TRUE

(hd <- has_disc(vaas_et_al))

##   [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [29] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [43] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [57] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [71] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [85] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [99] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [113] TRUE TRUE

stopifnot(d == c(114, 384, 96), ha, hd)

## Not run: 
##D 
##D # get the data subset used in Figure 1 in Vaas et al. (2012)
##D vaas.1.3 <- subset(vaas_et_al, query = list(Experiment = "First replicate",
##D   'Plate number' = 3))
##D 
##D # plot the data approximately as in Vaas et al. (2012)
##D xy_plot(vaas.1.3[, , c("D01", "D02", "C10", "C11")],
##D   main = "E. coli vs. P. aeruginosa", include = list("Species", "Strain"))
##D level_plot(vaas.1.3[, , c("D01", "D02", "C10", "C11")],
##D   main = "E. coli vs. P. aeruginosa", include = list("Species", "Strain"))
## End(Not run)