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Table 4 Comparison of detected peaks (ovarian cancer dataset)

From: Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

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
  1. 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.