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Multiplicative Signal Correction

Source: R/msc.R
msc.Rd

This function performs multiplicative scatter/signal correction (MSC) on an input data of spectra. It corrects for multiplicative and additive effects in the spectral data by regressing against a reference spectrum.

Usage

msc(
  x,
  xref = NULL,
  drop.offset = TRUE,
  robust = TRUE,
  window = NULL,
  drop.na = TRUE
)

Arguments

x

A numeric matrix or data frame containing the input spectra. Each row represents a sample, and each column represents a spectral variable.

xref

An optional numeric vector representing the reference spectrum. If NULL (default), the mean or median of x is used as the reference.

drop.offset

A logical value indicating whether the additive offset \(a_i\) should be removed from the spectra (default is TRUE). If FALSE, only the multiplicative effect is corrected: \(\textbf{x}_i / b_i\).

robust

A logical value indicating whether the median (TRUE, default) or the mean (FALSE) of x is used as xref.

window

An optional list of numeric vectors specifying the column indices of spectral windows. If provided, MSC is performed separately for each window.

drop.na

A logical value indicating whether to remove spectra (rows) containing missing values. If TRUE (the default), such rows are removed.

Value

A list with the following components:

correction

The corrected spectra.

offset

The intercepts/offsets \(a_i\) (a matrix with one column per window when window is given).

slope

The multiplicative scatter factors/slopes \(b_i\) (a matrix with one column per window when window is given).

reference

The reference spectrum used.

Details

Each spectrum \(\textbf{x}_i\) is regressed against the reference spectrum, \(\textbf{x}_i = a_i + b_i \textbf{x}_{ref} + \textbf{e}_i\), and corrected as \((\textbf{x}_i - a_i) / b_i\). When window is given, the regression and correction are carried out separately in each spectral window (piecewise MSC); variables outside all windows are left unchanged.

To correct new spectra consistently, pass the returned reference as xref.

Author

Christian L. Goueguel

Examples

data(forageLIBS)
spectra <- forageLIBS[-(1:14)]  # the spectral channels
res <- msc(spectra)
res$correction[1:3, 1:4]
#> # A tibble: 3 × 4
#>   `199.3771616` `199.4644141` `199.5516666` `199.6389192`
#>           <dbl>         <dbl>         <dbl>         <dbl>
#> 1          698.          709.          755.          708.
#> 2          664.          686.          716.          658.
#> 3          632.          650.          696.          650.