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

Table 5

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

Agilent/29K	Basal-like	HER2-enriched	Luminal A	Luminal B	Normal-like
Basal-like	42	0	0	1	1
HER2-enriched	1	25	0	1	1
Luminal A	0	2	84	5	5
Luminal B	1	2	8	49	0
Normal-like	3	0	3	1	8