montero_et_al: Example data set from Montero-Calasanz et al. (2013)

In opmdata: OmniLog(R) Phenotype Microarray Example Data

Description

This OPMS object contains a selection of the measurements used in two studies by Montero-Calasanz et al. (2013). A minimal set of metadata has been added to describe the conducted OmniLog(R) phenotype microarray (PM) experiments as far as necessary (see below). The plate type is ‘Generation III’, but the running mode was as for the usual PM plates.

Format

OPMS object with the dimensions 12 x 382 x 96, i.e. twelve plates with about 382 time points and 96 wells per plate. (Three quartets of plates with 292, 380 or 382 time points, respectively).

Details

The plates do not contain aggregated values generated via do_aggr. Rather, they serve as an exemplar for merging subsequent runs of the same physical plate prior to estimating curve parameters. See the example section below.

The metadata comprise the entries ‘Strain’ and ‘Replicate’, which describe all aspects necessary for serving as an exemplar. The data comprise three subsequent runs for each of the two replicates for each of the two strains, hence twelve plates. The two strains are the type strains of Geodermatophilus telluris (DSM 45421T) and Geodermatophilus tzadiensis (DSM 45416T), respectively.

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.

Montero-Calasanz, M.C., Goeker, M., Poetter, G., Rohde, M., Sproeer, C., Schumann, P., Gorbushina, A.A., Klenk, H.-P. 2013 Geodermatophilus telluris sp. nov., a novel actinomycete isolated from Saharan desert sand in Chad. International Journal of Systematic and Evolutionary Microbiology 13, 2254–2259.

Montero-Calasanz, M.C., Goeker, M., Broughton, W.J., Cattaneo, A., Favet, J., Poetter, G., Rohde, M., Sproeer, C., Schumann, P., Gorbushina, A.A., Klenk, H.-P. 2013 Geodermatophilus tzadiensis sp. nov., isolated Sahara desert sand in Chad. Systematic and Applied Microbiology 36, 177–182.

http://www.dsmz.de/catalogues/details/culture/DSM-45416.html

http://www.dsmz.de/catalogues/details/culture/DSM-45421.html

Examples

data(montero_et_al)
plate_type(montero_et_al) # should indicate generation-III plates
(d <- dim(montero_et_al))
(ha <- has_aggr(montero_et_al))
stopifnot(!ha, d == c(12, 382, 96))

## Overview of the metadata
to_metadata(montero_et_al)

## Splitting, merging, joining
x <- opms(lapply(split(montero_et_al, ~ Strain + Replicate), merge))
# Other datasets might need an adaption of the parsing of the setup time,
# and of course might contain other combinations of metadata entries that
# identify the physical plate.
x
stopifnot(is(x, "OPMS"), length(x) == 4)

## Not run: 
  xy_plot(x, include = ~ Strain + Replicate)
## End(Not run)

opmdata documentation built on May 2, 2019, 5:47 p.m.