Table 3.

Agreement between intrinsic gene sets and adjustment methods

Intrinsic genes	Kappa*	95% CI	Adjustment method	Kappa*	95% CI
Sørlie 500			Gene centring
Original data vs. gene centring	0.51	0.43-0.60	Sørlie 500 vs. Hu 306	0.58	0.50-0.67
Original data vs. DWD	0.49	0.41-0.57	Sørlie 500 vs. PAM50	0.52	0.43-0.61
Gene centring vs. DWD	0.83	0.77-0.90	Hu306 vs. PAM50	0.85	0.79-0.91
Hu 306			DWD adjusted
Original data vs. gene centring	0.51	0.43-0.58	Sørlie 500 vs. Hu 306	0.56	0.47-0.65
Original data vs. DWD	0.5	0.42-0.58	Sørlie 500 vs. PAM50	0.55	0.47-0.64
Gene centring vs. DWD	0.95	0.92-0.99	Hu306 vs. PAM50	0.67	0.59-0.76
PAM50
Original data vs. gene centring	0.8	0.73-0.87
Original data vs. DWD	0.66	0.58-0.75
Gene centring vs. DWD	0.67	0.58-0.75