process_plate: Process a Plate and Save Normalised Output to CSV

In SerolyzeR: Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data

Process a Plate and Save Normalised Output to CSV

Description

This function processes a plate and computes normalised values based on the specified normalisation_type. The function supports three types of normalisation:

• RAU (Relative Antibody Units) - Default normalisation type.

• nMFI (Normalised Median Fluorescence Intensity).

• MFI (Median Fluorescence Intensity, blank-adjusted raw MFI values).

Depending on the chosen normalisation type, the function:

• Adjusts for blanks (if blank_adjustment = TRUE).

• Computes the relevant normalised values for each analyte in the plate.

• Aggregates computed values into a single data frame.

• Optionally writes the results to a CSV file.

RAU Normalisation Workflow:

1. Blank adjustment (if enabled).

2. Fit standard curve models for each analyte.

3. Compute RAU values based on the fitted models.

4. Aggregate RAU values into a data frame.

5. Save the results to a CSV file.

nMFI Normalisation Workflow:

1. Blank adjustment (if enabled).

2. Compute nMFI values using the target dilution.

3. Aggregate nMFI values into a data frame.

4. Save the results to a CSV file.

MFI Normalisation Workflow:

1. Blank adjustment (if enabled).

2. Save the adjusted MFI values to a CSV file.

If the plate is already blank-adjusted, setting blank_adjustment = TRUE has no effect.

More details on the normalisation methods can be found in:

• RAU: create_standard_curve_model_analyte.

• nMFI: get_nmfi.

Usage

process_plate(
  plate,
  filename = NULL,
  output_dir = "normalised_data",
  write_output = TRUE,
  normalisation_type = "RAU",
  data_type = "Median",
  blank_adjustment = FALSE,
  verbose = TRUE,
  reference_dilution = 1/400,
  ...
)

Arguments

plate	(Plate) A plate object containing fluorescence intensity data.
filename	(character(1), optional) Output CSV filename. Defaults to ⁠{plate_name}_{normalisation_type}.csv⁠. If omitted (NULL), the filename is auto-generated. If the filename lacks .csv, the extension is automatically added. If output_dir is specified, it is combined with filename unless filename is an absolute path. If a file already exists at the path, it will be overwritten.
output_dir	(character(1), default = 'normalised_data') Directory for saving the output file. If the directory does not exist, it will be created. If NULL, the current working directory is used.
write_output	(logical(1), default = TRUE) Whether to save the output to a CSV file.
normalisation_type	(character(1), default = 'RAU') The normalisation method to apply. Allowed values: c(MFI, RAU, nMFI).
data_type	(character(1), default = 'Median') The data type to use for calculations.
blank_adjustment	(logical(1), default = FALSE) Whether to perform blank adjustment before computing values.
verbose	(logical(1), default = TRUE) Whether to print additional information during execution.
reference_dilution	(numeric(1) or character(1), default = 1/400) The target dilution used as a reference for nMFI normalisation. Ignored for RAU normalisation. Can be numeric (e.g., 0.0025) or a string ('1/400').
...	Additional arguments passed to the model fitting function (create_standard_curve_model_analyte).

Value

A data frame containing the computed normalised values.

Examples

plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "SerolyzeR")
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "SerolyzeR")
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
example_dir <- tempdir(check = TRUE)

# Process plate with default settings (RAU normalisation)
process_plate(plate, output_dir = example_dir)

# Process plate without blank adjustment, custom filename
process_plate(plate,
  filename = "plate_no_blank_adjustment.csv",
  output_dir = example_dir, blank_adjustment = FALSE
)

# Process plate with nMFI normalisation
process_plate(plate,
  output_dir = example_dir, normalisation_type = "nMFI",
  reference_dilution = 1 / 400
)

SerolyzeR documentation built on April 12, 2025, 2:11 a.m.