Microarray-Based RNA Profiling of Breast Cancer: Batch Effect Removal Improves Cross-Platform Consistency
Figure 3
Correlation and ICC analysis. Box plots illustrating the pair-wise sample-sample correlation coefficients when no adjustment was applied and after intraplatform adjustment for batch effects using ComBat for all 243 sample pairs using the 18424 shared genes (a) and pair-wise gene-gene correlation coefficients for all 18424 gene-pairs across all 243 samples (b). Box plots illustrating effects of intraplatform, between-platform adjustment, and high-variance genes on the pair-wise gene-gene ICC coefficient measured for all 18424 gene-pairs across all 243 samples (c).
