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Table 6 Comparison of the differential expression analysis on Hugene 1.0 ST arrays preprocessed with several popular algorithms

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 PM Student 0.72 0.74 0.61 0.83 0.83 0.67 0.54 0.61 0.65 0.73 0.72 0.75 0.74
   Win. t 0.82 0.82 0.69 0.89 0.86 0.70 0.57 0.71 0.69 0.80 0.77 0.80 0.77
   Reg. t 0.79 0.81 0.64 0.87 0.83 0.65 0.56 0.67 0.69 0.78 0.77 0.76 0.72
  PM Student 0.80 0.80 0.65 0.88 0.83 0.71 0.60 0.83 0.79 0.84 0.80 0.81 0.78
  Norm Win. t 0.85 0.85 0.69 0.90 0.86 0.71 0.59 0.85 0.81 0.86 0.83 0.84 0.79
   Reg. t 0.86 0.85 0.65 0.90 0.84 0.67 0.57 0.83 0.80 0.85 0.82 0.82 0.75
Plier Raw Student 0.86 0.74 0.75 0.90 0.85 0.78 0.52 0.74 0.71 0.83 0.77 0.85 0.80
   Win. t 0.90 0.83 0.79 0.92 0.89 0.80 0.59 0.77 0.74 0.85 0.81 0.87 0.82
   Reg. t 0.91 0.84 0.81 0.94 0.89 0.83 0.60 0.79 0.74 0.87 0.82 0.89 0.82
dChip Li-Wong MBEI PM Student 0.80 0.74 0.65 0.86 0.84 0.71 0.49 0.63 0.71 0.77 0.77 0.79 0.77
  Norm Win. t 0.85 0.80 0.71 0.88 0.86 0.72 0.54 0.69 0.73 0.81 0.81 0.81 0.78
   Reg. t 0.82 0.79 0.65 0.88 0.84 0.70 0.53 0.64 0.75 0.80 0.82 0.80 0.73
RMA Median-polish Norm Student 0.83 0.83 0.70 0.86 0.83 0.72 0.60 0.80 0.78 0.81 0.78 0.81 0.77
   Win. t 0.89 0.88 0.75 0.88 0.86 0.73 0.60 0.83 0.80 0.84 0.81 0.83 0.79
   Reg. t 0.93 0.92 0.80 0.93 0.90 0.77 0.63 0.87 0.84 0.89 0.85 0.88 0.84
GCRMA Median-polish Raw Student 0.84 0.86 0.76 0.82 0.88 0.53 0.64 0.41 0.69 0.75 0.76 0.69 0.81
   Win. t 0.87 0.89 0.79 0.86 0.87 0.56 0.60 0.49 0.68 0.80 0.75 0.73 0.79
   Reg. t 0.90 0.91 0.84 0.88 0.90 0.65 0.62 0.44 0.70 0.84 0.77 0.74 0.82
  Norm Student 0.85 0.85 0.78 0.89 0.86 0.71 0.68 0.83 0.82 0.84 0.82 0.80 0.80
   Win. t 0.89 0.88 0.80 0.89 0.86 0.70 0.62 0.84 0.80 0.84 0.81 0.82 0.79
   Reg. t 0.94 0.94 0.86 0.95 0.92 0.75 0.66 0.89 0.86 0.90 0.86 0.88 0.84
  1. We analyzed the Hugene 1.0 ST Tissue Mixture Study (Affymetrix) for differential expression, using Student t-test, Regularized t-test, and Window t-test. Several previously published preprocessing methods were tested. 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 highlights the top 5 correlation coefficients for each column. Raw/Norm labels refer to raw and normalized data, PM stands for PM-only methods.