# Msc settings gui

The MSC Settings GUI allows you to select options relevant to the use of applying Multiplicative Scatter Correction (MSC) to your data. See the mscorr wiki page for more information on the underlying function.

**Reference Data**:

Reference or "target" spectrum that the data is regressed against. Default is to use the mean of the data (If the **median** algorithm is selected then the median of the data is used as the reference and not the mean). Use the **Load** button to load a reference vector of type double.

**Use Intercept**:

This is a flag indicating if an offset should be removed from the spectra in addition to correcting scaling. If checked then the offset is corrected, if unchecked then the offset is not removed. Default is to correct for offset.

**Spectral Mode**:

Defines which mode of the data is the spectral mode (default = 2) and is only editable when the data contains 3 or more modes.

**Window**:

Allows for scatter correction in spectral "windows" that can be of different widths. Use the **Select** button to enter variable index values or to graphically select regions. Use the **All Variables** button to reset the window selection to use all variables. MSC is will be performed in each of the windows (alpha and beta are not assigned). The standard approach is to use the entire spectrum. When using windows, subindices cannot be selected.

Example of how to enter indices:

**Subindices**:

Specifies the indices within the included spectral variables that are used to calculate the MSC correction. The default is that ALL included spectral variables are used. Correction is always applied to the entire spectrum even if subindices are used to calculate the correction factors. When using subindices, windows cannot be selected.

**Algorithm**:

Specifies how the spectrum scale factors are determined. The default is by **least squares** regression between each spectrum and the reference spectrum. If **median** is selected then the median of the ratio between a spectrum and the reference. If median is used the offset is not removed (**Use Intercept** becomes unchecked), and if no reference is given then the median of the data is used as the reference. Median is only appropriate if most values are non-negative.

**See also:**