Microarray-Based RNA Profiling of Breast Cancer: Batch Effect Removal Improves Cross-Platform Consistency

Table 4

Association between PAM50 molecular subtype classifications in the Agilent and the 29K dataset (unadjusted).

Agilent/29K	Basal-like	HER2-enriched	Luminal A	Luminal B	Normal-like
Basal-like	42	0	1	1	0
HER2-enriched	0	27	0	1	0
Luminal A	0	3	83	4	6
Luminal B	0	7	10	43	0
Normal-like	3	0	4	0	8