Table 1. Summary of variability and aggregated correlation values for different within- and cross-platform normalisation.

	Cross-platform						Within-platform
	Standardi-sation		ComBat		XPN		PMOnly		Loess Only		PMLoess
	SC	DC	SC	DC	SC	DC	SC	DC	SC	DC	SC	DC
Variability between replicates	↑ with PML; ↓ with PM & L	↑ with PM & PML; ↓ with L	↑ with PM & L; ↓ with PML	↑ with L; ↓ with PM & PML	↑ with PM & L; ↓ with PML	↓	↑	↑	↓	↓	↓	↓
Amplitude of noise frequencies	↑ with PM & PML; ↓ with L		↑ with L; ↓ with PM & PML		↑ with L; ↓ with PM & PML		↑		↓		↓
Number of highly correlated genes	↑	↑	↑	↑	↓	↓	↑	↑ in PL & PS; ↓ in S	↓	↓	↑	↑ in S; ↓ in PS & PL
Average absolute correlation	↑	↑	↑	↑	↓	↓	↑	↓	↓	↑	↑	↑

SC and DC identify results for single- and dual-channel datasets; PL, PS and S represent the three dual-channel datasets (PramilaL, PramilaS and Spellman), while PM, PML, L stand for PMOnly, PMLoess and LoessOnly, respectively. Arrows indicate whether variability and correlations are increased (↑) or decreased (↓) relative to the other normalisation procedures in the same category (cross- or within-platform).