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Posts tagged “autoscaling

Comparison of Serum vs Urine metabolites +

Primary metabolites in human serum or urine.

serum urine idOh oh, there seem to be some outliers: serum samples  looking like urine and vice versa. Fix these and evaluate using PCA and hierarchical clustering on rank correlations.

fix assignments

Now things look more believable. Next let us test the effects of data pre-treatment on PLS-DA model scores for a 3 group comparison in serum. Ideally group scores would be maximally resolved in the dimension of the first latent variable (x) and inter-group variance would be orthogonal or in the y-axis.

scaling vs normalization

Compared to raw data (TOP) where ~ 3 top variables (glucose, urea and mannitol) dominate the variance structure, the autoscaled model, due to variable-wise  mean subtraction and division by the standard deviation, displays a more balanced contribution to scores variance by variables. The larger separation between  WHITE  and RED class scores  along the x-axis suggest  improved classifier performance over raw data model and overview of samples with scores outside their respective group’s Hotelling’s T ellipse (95%) might point to  a sample outlier to further investigate or potentially exclude from the current test.