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Table 2 Comparison of the differential expression analysis on HG-U133Plus2 arrays preprocessed with affyILM and popular summarization procedures

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

Summary 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
Average difference Raw Student 0.73 0.69 0.57 0.81 0.81 0.54 0.51 0.62 0.67 0.72 0.75 0.69 0.68
   Win. t 0.83 0.83 0.72 0.87 0.90 0.60 0.65 0.71 0.77 0.79 0.85 0.76 0.80
   Reg. t 0.75 0.81 0.67 0.84 0.89 0.56 0.61 0.72 0.72 0.78 0.82 0.76 0.77
  Scaled Student 0.72 0.69 0.56 0.76 0.80 0.48 0.57 0.63 0.72 0.63 0.73 0.66 0.74
   Win. t 0.85 0.83 0.73 0.86 0.89 0.56 0.68 0.73 0.81 0.74 0.83 0.74 0.83
   Reg. t 0.81 0.79 0.67 0.83 0.87 0.49 0.63 0.68 0.76 0.69 0.79 0.69 0.78
Li-Wong MBEI Raw Student 0.71 0.69 0.57 0.78 0.77 0.53 0.45 0.61 0.68 0.69 0.74 0.69 0.67
   Win. t 0.81 0.82 0.72 0.84 0.86 0.58 0.62 0.69 0.77 0.77 0.83 0.75 0.79
   Reg. t 0.73 0.79 0.67 0.81 0.84 0.54 0.58 0.68 0.74 0.74 0.81 0.73 0.77
  Scaled Student 0.68 0.65 0.52 0.68 0.73 0.43 0.54 0.57 0.65 0.54 0.67 0.60 0.67
   Win. t 0.81 0.79 0.70 0.80 0.83 0.51 0.66 0.66 0.76 0.67 0.79 0.67 0.77
   Reg. t 0.77 0.75 0.63 0.76 0.80 0.46 0.61 0.62 0.71 0.62 0.75 0.63 0.71
1-Step Tukey-Biweight Raw Student 0.78 0.74 0.64 0.85 0.84 0.61 0.51 0.66 0.71 0.77 0.79 0.76 0.71
   Win. t 0.86 0.86 0.77 0.90 0.92 0.65 0.68 0.73 0.80 0.83 0.89 0.80 0.83
   Reg. t 0.78 0.85 0.74 0.87 0.91 0.62 0.65 0.74 0.77 0.82 0.87 0.80 0.81
  Scaled Student 0.76 0.73 0.61 0.78 0.83 0.54 0.63 0.65 0.74 0.66 0.76 0.71 0.77
   Win. t 0.87 0.86 0.78 0.89 0.92 0.61 0.74 0.74 0.83 0.77 0.86 0.77 0.85
   Reg. t 0.86 0.84 0.74 0.87 0.90 0.55 0.69 0.70 0.80 0.73 0.83 0.74 0.82
Median Raw Student 0.73 0.69 0.57 0.81 0.81 0.54 0.51 0.62 0.67 0.72 0.76 0.69 0.68
   Win. t 0.83 0.83 0.72 0.87 0.90 0.59 0.65 0.70 0.77 0.79 0.85 0.75 0.80
   Reg. t 0.76 0.81 0.68 0.85 0.89 0.55 0.61 0.70 0.74 0.77 0.83 0.75 0.78
  Scaled Student 0.72 0.69 0.56 0.76 0.80 0.48 0.57 0.63 0.72 0.63 0.73 0.66 0.74
   Win. t 0.85 0.83 0.73 0.86 0.90 0.55 0.69 0.72 0.81 0.74 0.84 0.74 0.83
   Reg. t 0.82 0.80 0.68 0.83 0.87 0.50 0.64 0.68 0.77 0.70 0.80 0.70 0.79
Median-polish Raw Student 0.85 0.81 0.73 0.88 0.88 0.70 0.52 0.70 0.76 0.82 0.83 0.80 0.74
   Win. t 0.91 0.90 0.85 0.92 0.94 0.73 0.70 0.75 0.83 0.87 0.91 0.82 0.86
   Reg. t 0.90 0.89 0.86 0.93 0.94 0.74 0.70 0.75 0.85 0.88 0.90 0.83 0.87
  Scaled Student 0.80 0.77 0.66 0.79 0.83 0.56 0.65 0.65 0.73 0.66 0.76 0.71 0.76
   Win. t 0.91 0.90 0.85 0.90 0.92 0.67 0.78 0.76 0.84 0.80 0.87 0.80 0.87
   Reg. t 0.93 0.91 0.86 0.91 0.94 0.65 0.80 0.76 0.86 0.79 0.89 0.81 0.90
  1. We analyzed the HG-U133plus2 Tissue Mixture Study (Affymetrix) for differential expression, using Student t-test, Regularized t-test, and Window t-test. Summarization tests were performed on probe concentrations computed with AffyILM. Comparison between heart (mix 1) and brain (mix 9) is assumed to provide the reference list of p-values. For each combination of summarization/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/Scaled labels respectively refers to summarization tests performed with/without a scaling step between arrays.