Table 4.

Comparison of detected peaks (ovarian cancer dataset)

CM10
Peak (Ciphergen)	logFC	p-value	adjusted p	Peak (Cromwell)	logFC	p-value	adjusted p	cor
1546.06	-0.55	0.004	0.065	1540.24	-0.47	0.001	0.039	0.73
1555.67	-0.83	0.001	0.039	1552.28	-0.39	0.011	0.093	0.77
1584.26	-0.52	0.001	0.034	1540.24	-0.47	0.001	0.039	0.87
2648.88	-0.73	0.001	0.029	1540.24	-0.47	0.001	0.039	0.63
2747.67	-1.28	<0.001	0.008	2747.56	-1.06	0.001	0.039	0.95
2785.04	-1.21	<0.001	0.008	2785.52	-1.08	0.003	0.051	0.95
2824.21	-0.73	0.002	0.044	2823.75	-0.62	0.018	0.105	0.86
3164.30	-0.84	0.001	0.025	3163.52	-0.64	0.013	0.098	0.83
3403.11	-0.81	0.002	0.039	3402.37	-0.68	0.014	0.099	0.93
3441.36	-0.75	0.001	0.031	1615.29	-0.37	0.011	0.093	0.77
Q10
Peak (Ciphergen)	logFC	p-value	adjusted p	Peak (Cromwell)	logFC	p-value	adjusted p	cor
1721.35	-0.68	0.004	0.046	1511.76	-0.34	0.175	0.439	0.31
4078.66	-0.42	0.015	0.125	4079.56	-0.34	0.155	0.439	0.72
4273.34	-0.48	0.012	0.113	4274.66	-0.28	0.236	0.439	0.75
4287.14	-1.06	<0.001	0.005	4287.39	-0.92	0.009	0.143	0.88
6889.71	-1.02	0.001	0.014	6889.77	-1.43	0.004	0.103	0.92
8574.28	-1.47	<0.001	0.010	8572.2	-1.51	0.004	0.103	0.96
8703.04	-1.05	0.006	0.063	8700.12	-0.96	0.020	0.143	0.95
8772.14	-1.26	<0.001	0.001	8776.73	-1.35	0.004	0.103	0.91
13782.2	-1.11	0.002	0.029	6889.77	-1.43	0.004	0.103	0.91
28143.3	-0.77	0.016	0.125	8682.97	-1.09	0.015	0.143	0.75

List of ten most differentially expressed m/z values after pre-processing with either Ciphergen or Cromwell (setting C) for CM10 and Q10 ProteinChip arrays. For each of the m/z values the log₂ fold change (logFC), p-value and adjusted p-value are given. Peaks were matched between Ciphergen and Cromwell by calculating Pearson's correlation between a Ciphergen peak profile and all Cromwell peak profiles. The Cromwell peak with highest Pearson's correlation is considered to be a matching peak. Last column gives the corresponding correlation value.