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Table 5 Comparison of the differential expression analysis on HG-U133Plus2 arrays preprocessed with popular methods

From: From hybridization theory to microarray data analysis: performance evaluation

Method Data Diff. expr. m2 m8 m3 m7 m4 m6 m1 m6 m4 m9 m1 m4 m6 m9 m1 m5a m5a m9 m1 m5b m5b m9 m1 m5c m5c m9
MAS 5 1-Step Tukey-Biweight Bg Student 0.71 0.67 0.54 0.74 0.82 0.45 0.58 0.54 0.70 0.62 0.75 0.60 0.73
   Win. t 0.83 0.81 0.69 0.85 0.89 0.51 0.66 0.62 0.78 0.71 0.83 0.68 0.81
   Reg. t 0.83 0.79 0.68 0.85 0.88 0.45 0.61 0.57 0.77 0.69 0.83 0.65 0.78
  Bg Student 0.80 0.79 0.69 0.83 0.86 0.62 0.69 0.78 0.82 0.78 0.82 0.79 0.83
  Norm Win. t 0.89 0.88 0.79 0.90 0.92 0.66 0.73 0.84 0.88 0.84 0.88 0.84 0.88
   Reg. t 0.89 0.88 0.77 0.89 0.91 0.61 0.71 0.82 0.86 0.83 0.87 0.83 0.87
  PM Student 0.72 0.70 0.56 0.77 0.85 0.52 0.59 0.57 0.72 0.68 0.80 0.62 0.73
   Win. t 0.82 0.82 0.72 0.87 0.93 0.59 0.69 0.66 0.80 0.77 0.88 0.68 0.80
   Reg. t 0.76 0.77 0.67 0.84 0.90 0.52 0.62 0.60 0.77 0.73 0.86 0.62 0.76
  PM Student 0.84 0.82 0.73 0.86 0.89 0.66 0.75 0.77 0.84 0.79 0.85 0.82 0.86
  Norm Win. t 0.91 0.90 0.83 0.92 0.94 0.69 0.79 0.82 0.88 0.85 0.91 0.86 0.91
   Reg. t 0.90 0.89 0.79 0.91 0.92 0.64 0.75 0.79 0.85 0.82 0.88 0.84 0.87
Plier Raw Student 0.73 0.71 0.56 0.75 0.82 0.57 0.56 0.64 0.70 0.71 0.76 0.67 0.71
   Win. t 0.82 0.80 0.70 0.83 0.87 0.60 0.63 0.67 0.74 0.76 0.82 0.70 0.77
   Reg. t 0.82 0.80 0.70 0.85 0.87 0.65 0.64 0.71 0.72 0.80 0.81 0.73 0.75
dChip Li-Wong MBEI PM Student 0.82 0.81 0.70 0.81 0.86 0.63 0.73 0.73 0.80 0.71 0.81 0.78 0.82
  Norm Win. t 0.88 0.87 0.79 0.86 0.89 0.63 0.76 0.73 0.82 0.74 0.84 0.79 0.85
   Reg. t 0.88 0.86 0.73 0.85 0.88 0.58 0.73 0.70 0.78 0.70 0.81 0.77 0.81
  Norm Student 0.80 0.79 0.72 0.80 0.84 0.59 0.71 0.74 0.80 0.73 0.81 0.74 0.80
   Win. t 0.86 0.85 0.79 0.84 0.87 0.61 0.73 0.76 0.82 0.76 0.84 0.77 0.83
   Reg. t 0.84 0.84 0.75 0.83 0.86 0.54 0.71 0.73 0.81 0.73 0.82 0.74 0.81
qFARMS Norm Student 0.81 0.80 0.72 0.81 0.85 0.65 0.71 0.73 0.79 0.73 0.81 0.77 0.81
   Win. t 0.85 0.84 0.73 0.81 0.84 0.54 0.64 0.69 0.77 0.70 0.79 0.71 0.78
   Reg. t 0.89 0.89 0.77 0.85 0.89 0.56 0.69 0.76 0.83 0.75 0.84 0.76 0.83
lFARMS Norm Student 0.81 0.79 0.70 0.79 0.84 0.62 0.64 0.72 0.73 0.72 0.78 0.76 0.80
   Win. t 0.85 0.84 0.73 0.81 0.84 0.54 0.60 0.68 0.72 0.70 0.76 0.70 0.77
   Reg. t 0.89 0.88 0.75 0.83 0.89 0.52 0.66 0.69 0.78 0.68 0.82 0.72 0.83
RMA Median-polish Norm Student 0.83 0.82 0.73 0.82 0.86 0.65 0.72 0.75 0.81 0.75 0.82 0.78 0.82
   Win. t 0.92 0.91 0.85 0.90 0.92 0.71 0.79 0.82 0.86 0.84 0.88 0.84 0.88
   Reg. t 0.93 0.93 0.87 0.92 0.93 0.73 0.79 0.84 0.88 0.86 0.90 0.86 0.89
GCRMA Median-polish Raw Student 0.85 0.84 0.76 0.83 0.89 0.57 0.72 0.49 0.78 0.61 0.84 0.69 0.83
   Win. t 0.90 0.88 0.84 0.90 0.92 0.62 0.75 0.57 0.80 0.68 0.86 0.73 0.85
   Reg. t 0.91 0.90 0.86 0.91 0.93 0.66 0.76 0.60 0.80 0.71 0.86 0.76 0.84
  Norm Student 0.87 0.86 0.80 0.86 0.89 0.68 0.75 0.82 0.86 0.81 0.86 0.81 0.86
   Win. t 0.92 0.92 0.86 0.90 0.92 0.69 0.78 0.85 0.88 0.85 0.89 0.84 0.89
   Reg. t 0.94 0.94 0.89 0.92 0.95 0.71 0.79 0.87 0.91 0.87 0.92 0.86 0.91
  1. We analyzed the HG-U133plus2 Tissue Mixture Study (Affymetrix) for differential expression, using Student t-test, Regularized t-test, and Window t-test. Several previously published preprocessing methods were compared. Comparison between heart (mix 1) and brain (mix 9) is assumed to provide the reference list of p-values. For each combination of preprocessing/analysis steps (rows), Pearson's correlation coefficient has been computed on log10(p-values) between the reference analysis and several comparisons of mixtures (columns). Underlined characters highlight the top 5 correlation coefficients for each column. Raw/Norm labels refer to raw and normalized data, PM stands for PM-only and Bg refers to background correction (using MM).