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

Table 5

Association of clinical ER and HER2 status with intrinsic taxonomy, classified by either PAM50 single sample prediction or PLS-regression.

	Basal	HER2	LumA	LumB	Norm
ER	PAM50 SSP
Negative	40	28	0	3	9
Positive	0	7	67	46	7
HER2
Normal	37	5	63	30	8
Over-expression	3	30	4	19	8
ER	PLS-regression
Negative	38	19	1	1	3
Positive	0	5	59	33	2
HER2
Normal	35	0	56	21	4
Over-expression	3	24	4	13	1

SSP: single sample prediction, Basal: basal-like, HER2: Her2-enriched, LumA: luminal-A, LumB: luminal-B, Norm: normal breast-like subtype.