Table 2.

Performance of different cleaning approaches when there is moderate genuine correlation between genes (based on 1000 simulation runs)

Method	Raw	BC	BC+QN	RUV-random
% WS	48.2	48.1	48.0	0.7
FN2	0.423	0.420	0.414	0.005

The performance was measured using the proportion of estimates with the wrong sign (WS). While FN² refers to a squared Frobenius norm (FN²) measure (explained in the text), which should be close to 0. All parameter choices and details of the simulation can be found in Additional file 1. All standard deviations for FN² were <0.001