Multiclass Prediction with Partial Least Square Regression for Gene Expression Data: Applications in Breast Cancer Intrinsic Taxonomy

Table 1

Performance of PLS-regression classifiers for prototypical arrays.

Intrinsic subtype	Basal-like	HER2-enriched	Luminal-A	Luminal-B	Normal breast-like
Number of samples	57	35	23	12	12
PLS-regression
Number of gene component	1	1	2	1	2
𝑋-variance explained	57.0%	37.1%	74.5%	25.8%	60.2%
𝑌-variance explained	86.7%	56.2%	64.6%	24.6%	66.5%
Binary LR
Adjusted 𝑅-square	0.99	0.73	0.9	0.63	0.99
AUC	1	0.96	0.99	0.96	1
Accuracy	98.6%	89.9%	97.1%	95.0%	100.0%
Sensitivity	98.2%	74.3%	91.3%	50.0%	100.0%
Specificity	98.8%	95.2%	98.3%	99.2%	100.0%

PLS: partial least square, LR: logistic regression, AUC: area under the curve.