Microarray-Based RNA Profiling of Breast Cancer: Batch Effect Removal Improves Cross-Platform Consistency
Figure 2
PCA plots showing all 243 samples analyzed using the 29K array platform prior to ((a) and (c)) and after batch-effect adjustment using ComBat method ((b) and (d)). Colors in (a) and (b) correspond to the different fabrication batches. Colors in (c) and (d) correspond to the molecular breast cancer subtypes classified using PAM50 subtype classifier.
