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

Table 2

Prediction of ER status by ESR1 expression levels in the Agilent dataset and the 29K dataset.

Platform	Number of samples	Cutoff	Sensitivity; (TP)	Specificity; (TN)	Accuracy
Agilent dataset	177 vs. 54	1.6	0.82 (44)	0.96 (169)	0.89
29K dataset (no adjustment)	177 vs. 54	1.6	0.82 (44)	0.94 (167)	0.88
29K dataset (intraplatform adj.)	177 vs. 54	1.6	0.82 (44)	0.94 (167)	0.88