Table 5. Number of TP and FP found in the different simulations for the unbalanced study design dataset.

Norm.	QCs	Subjects	N Batches	Effect	N effect genes	Gamma	Error	LMM		LM		LMBatch		Lmcom
								TP	FP	TP	FP	TP	FP	TP	FP
Batch	No	251	14	3	500	2.72	0	500.0	79.2	500.0	7383.9	500.0	76.4	499.6	34.8
Batch	Yes	251	14	3	500	2.72	0	500.0	80.3	500.0	7374.6	500.0	76.4	499.5	34.6
Batch	No	251	14	1	500	2.72	0	500.0	79.2	467.6	7366.9	500.0	76.4	485.1	34.9
Batch	Yes	251	14	1	500	2.72	0	500.0	87.0	470.2	6104.1	500.0	83.0	480.9	43.2
Batch	No	251	14	0.5	500	2.72	0	497.9	78.9	235.5	7358.1	497.4	75.9	448.3	35.0
Batch	Yes	251	14	0.5	500	2.72	0	498.0	80.0	239.1	7347.7	497.4	75.9	447.6	34.7
Batch	No	251	14	0.4	500	2.72	0	492.6	78.2	185.3	7357.4	491.7	75.2	429.8	34.9
Batch	Yes	251	14	0.4	500	2.72	0	492.9	79.3	191.3	7343.4	491.7	75.2	429.3	34.7
Batch	No	251	14	0.3	500	2.72	0	471.5	75.7	144.8	7356.8	469.7	72.8	394.1	34.7
Batch	Yes	251	14	0.3	500	2.72	0	472.1	76.9	156.8	7336.9	469.7	72.8	393.6	34.4
Batch	No	251	14	0.2	500	2.72	0	383.6	68.1	127.3	7355.5	381.0	65.3	304.9	33.3
Batch	Yes	251	14	0.2	500	2.72	0	384.5	69.1	138.7	7325.3	381.0	65.3	304.5	33.0
Batch	No	251	14	0.1	500	2.72	0	89.8	36.2	132.2	7533.2	88.5	35.7	66.0	25.6
Batch	Yes	251	14	0.1	500	2.72	0	90.9	37.4	139.6	7633.8	88.5	35.7	65.9	21.4