wittmann_et_al: Example data set from Wittmann et al. (2014)
In opmdata: OmniLog(R) Phenotype Microarray Example Data

Description Format Details References Examples

This OPMS object contains the measurements used in the study by Wittmann et al. (2014). 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.

OPMS object with the dimensions 41 x 382 x 96, i.e. 41 plates with about 382 time points and 96 wells per plate. (38 plates have 384 time points; three plates have 382 time points).

All plates also contain aggregated values generated via do_aggr using the "opm-fast" method without bootstrapping.

For 62 strains of the opportunistic pathogenic bacterium Achromobacter xylosoxidans PM experiments were conducted with Generation-III plates using inoculation fluid IF-A. All plates were incubated in the left plate sliding carriage of the OmniLog(R) reader.

In addition to ‘genus’, ‘species’ and ‘strain’, the following metadata entries are contained in the wittmann_et_al OPMS object:

country: Lists the geographical origin.
city: Lists the city where the strain was isolated.
year: Lists the year in which the strain was isolated.
isolated_from: Lists the scientist who isolated the strain.
source: Distinguishes between environmental or clinical origin, if known.
habitat: Lists details on the habitat, if known.
replicate: Lists the number of experimental plate replicates per strain. 2-3 replicates per strain were performed.
MLSTcluster: Name of phylogenetic cluster to which a strain is affiliated. See reference Wittmann et al (2014).

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.

Wittmann, J., Dreiseikelmann, B., Rohde, C., Rohde, M., Sikorski, J. 2014 Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitious and opportunistic pathogen Achromobacter xylosoxidans. PLoS ONE 9, e86935.

data(wittmann_et_al)
plate_type(wittmann_et_al) # should indicate generation-III plates
(d <- dim(wittmann_et_al))
(ha <- has_aggr(wittmann_et_al))
stopifnot(d == c(41, 382, 96), ha)

## Brief overview of the metadata
head(to_metadata(wittmann_et_al))