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

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

## [1] "PM01"

(d <- dim(montero_et_al))

## [1]  12 382  96

(ha <- has_aggr(montero_et_al))

##  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [12] FALSE

stopifnot(!ha, d == c(12, 382, 96))

## Overview of the metadata
to_metadata(montero_et_al)

##    Strain Replicate Number
## 1   45416         A      1
## 2   45416         A      2
## 3   45416         A      3
## 4   45416         B      4
## 5   45416         B      5
## 6   45416         B      6
## 7   45421         A      7
## 8   45421         B      8
## 9   45421         A      9
## 10  45421         A     10
## 11  45421         B     11
## 12  45421         B     12

## 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

## 1
## Class                 OPM
## From file             /home/goeker/Documents/Phenotype/PM/Input_examples/Carmen_Montero/_45416_A_1_28_PMX_357_3_12_2012_A_15A_1.csv
## Hours measured        263.25
## Number of wells       96
## Plate type            PM01
## Position              15-A
## Setup time            3/12/2012 11:35:20 AM
## Metadata              3
## Aggregated            FALSE
## Discretized           FALSE
## 
## 2
## Class                 OPM
## From file             /home/goeker/Documents/Phenotype/PM/Input_examples/Carmen_Montero/_45416_B_1_28_PMX_357_3_12_2012_A_14A_0.csv
## Hours measured        263.25
## Number of wells       96
## Plate type            PM01
## Position              14-A
## Setup time            3/12/2012 11:35:20 AM
## Metadata              3
## Aggregated            FALSE
## Discretized           FALSE
## 
## 3
## Class                 OPM
## From file             /home/goeker/Documents/Phenotype/PM/Input_examples/Carmen_Montero/_45421._A_1_28_PMX_357_3_12_2012_A_21A_7.csv
## Hours measured        263.25
## Number of wells       96
## Plate type            PM01
## Position              21-A
## Setup time            3/12/2012 11:35:20 AM
## Metadata              3
## Aggregated            FALSE
## Discretized           FALSE
## 
## 4
## Class                 OPM
## From file             /home/goeker/Documents/Phenotype/PM/Input_examples/Carmen_Montero/_45421._B_1_28_PMX_357_3_12_2012_A_20A_6.csv
## Hours measured        263.25
## Number of wells       96
## Plate type            PM01
## Position              20-A
## Setup time            3/12/2012 11:35:20 AM
## Metadata              3
## Aggregated            FALSE
## Discretized           FALSE
## 
## => OPMS object with 4 plates (0 aggregated, 0 discretized) of type 'PM01', 96 well(s) and about 1054 time point(s).

stopifnot(is(x, "OPMS"), length(x) == 4)

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