rl_calc_decon_matrix: Calculate a Deconvolution Matrix

In BradyAJohnston/reluxr: Deconvolute Luminescence Readings on Bacterial Culture Plates

Calculate a Deconvolution Matrix

Description

Use the data from a calibration plate, where the plate is empty except for a single well with a luminescent signal, to create a deconvolution matrix that can be used to adjust other experimental results.

Usage

rl_calc_decon_matrix(
  data,
  value,
  b_noise,
  time = "time",
  ref_well = "I05",
  well = "well"
)

Arguments

data	A data frame that contains the data of the calibration plate.
value	Name of the column containing the luminescent values.
b_noise	The value of the background noise, which is the average signal for the background wells that are far away from the reference well.
time	Name of the column with the time values.
ref_well	The well ID of the reference well (i.e. 'E05', 'I12")
well	Name of the column with the well ID values.

Details

The deconvolution matrix will be unique for each plate type and plate-reader, so a matrix should be calculated for each combination of plate and plate reader, but once this is calculated, it can be re-used to adjust future experimental results.

Value

a deconvolution matrix, for use in rl_adjust_plate()

Examples

fl <- system.file(
  "extdata",
  "calibrate_tecan",
  "calTecan1.xlsx",
  package = "reluxr"
)

dat <- plate_read_tecan(fl)

dat

mat_d <- dat |>
  dplyr::filter(signal != "OD600") |>
  dplyr::filter(time_s > 500) |>
  rl_calc_decon_matrix(value, time_s, ref_well = "E05", b_noise = 30)

image(log10(mat_d))

BradyAJohnston/reluxr documentation built on March 20, 2023, 5:09 a.m.