Fig. 5

a Hierarchical Clustering (HCL) based on protein expression: Batch effects dominate here, as samples separate more strongly based on batch than by class. No variable selection was performed prior. b Principal Components (PCs) 1 and 2 stratified by class and batch: Although PC1 is still strongly associated with batch; there is also some association with class effects. In contrast, PC2 is strongly associated with class rather than with batch effects. c HCL based on all PCs: In this case, it is clear that batch effects dominate. d HCL following PC1 removal: Removal of PC1 appears to eradicate a large proportion of the batch effects. But this is incomplete, suggesting that there may still be ambient batch effects remaining