Quick guide to pre-processing

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Sugar mixture data

• Purpose

To show how to use pre-processing in LatentiX. A PCA model will be developed on near infrared (NIR) spectroscopy measurements on 231 mixtures of three constituents: glucose, fructose and sucrose.

The sample set was made according to a mixture design where the concentrations of all three constituents are varied between 0% (w/w) and 100% (w/w):

The crystalline samples were measured in a NIR Systems 6500 instrument (reflection) furnished with a sample cup (3 cm in diameter). The spectral range covered is 1100 nm to 2496 nm (every 4th nm); in total 350 data points per spectrum.

• Data

The dimension of the data structure is 231x350 variables. Three classes (as well as labels) are assigned the concentrations of fructose, glucose and sucrose.

100 %Fructose

100 %Sucrose

100 %Glucose

100 %Fructose

100 %Sucrose

100 %Glucose

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Plot the spectra

Select the predefined sets: Samples and NIR spectra

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Use wavelengths as the x-axis

First click on Variable number

Then select Wavelengths (nm)and click OK

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Now the x-axis is in nm

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Mean center the data

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Calculate a PCA model

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Plot the scores

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Color according to fructose

First select ContinuousThen select Fructose

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Name the PCA model

Click on Name

Then type name and click OK

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Make an SNV transformation

Note: you can select Show plot to see the effect on the data

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Calculate a PCA model

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Name the model

Click on Name

Then type name and click OK

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Plot the scores

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Scores plot – color by fructose concentration

First select ContinuousThen select Fructose

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Scores plot – color by glucose concentration

Then select Glucose

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Scores plot – color by sucrose concentration

Then select Sucrose

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Remove SNV transformation

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Make an MSC transformation

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Calculate a PCA model

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Name the model

Click on Name

Then type name and click OK

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Remove MSC transformation

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Calculate first derivatives

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Input to first derivatives

Window size

Polynomial order

Derivative calculated

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Calculate PCA model

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Name the model

Click on Name

Then type name and click OK

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The four models with different pre-processing can now be investigated and compared

THE END