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Table 4 Comparison of the differential expression analysis between HG-U133Plus2 and Hugene 1.0 ST arrays preprocessed with affyILM and several summarization procedures

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

Summary Data Diff. expr. m1 m9 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 0.46 0.44 0.37 0.30 0.43 0.42 0.41 0.28 0.47 0.44 0.46 0.43 0.44 0.37
   Win. t 0.54 0.52 0.46 0.39 0.51 0.52 0.50 0.36 0.55 0.53 0.55 0.52 0.53 0.48
   Reg. t 0.47 0.43 0.37 0.35 0.46 0.46 0.48 0.29 0.50 0.44 0.48 0.43 0.48 0.42
  Scaled Student 0.42 0.42 0.45 0.33 0.43 0.43 0.34 0.32 0.37 0.40 0.40 0.40 0.36 0.37
   Win. t 0.53 0.53 0.54 0.43 0.52 0.53 0.43 0.40 0.46 0.50 0.50 0.50 0.45 0.49
   Reg. t 0.46 0.46 0.49 0.39 0.45 0.48 0.39 0.34 0.38 0.42 0.41 0.42 0.39 0.43
Li-Wong MBEI Raw Student 0.47 0.40 0.38 0.33 0.45 0.46 0.41 0.32 0.47 0.48 0.47 0.46 0.43 0.38
   Win. t 0.52 0.49 0.44 0.42 0.50 0.53 0.49 0.38 0.53 0.56 0.53 0.54 0.50 0.50
   Reg. t 0.46 0.43 0.39 0.41 0.46 0.48 0.47 0.33 0.49 0.51 0.50 0.50 0.47 0.47
  Scaled Student 0.38 0.39 0.43 0.35 0.40 0.43 0.32 0.34 0.33 0.41 0.36 0.42 0.32 0.39
   Win. t 0.49 0.49 0.52 0.44 0.49 0.53 0.40 0.43 0.42 0.51 0.46 0.52 0.43 0.52
   Reg. t 0.42 0.41 0.47 0.41 0.44 0.48 0.36 0.37 0.38 0.48 0.42 0.48 0.39 0.49
1-Step Tukey-Biweight Raw Student 0.52 0.50 0.42 0.36 0.49 0.49 0.50 0.36 0.54 0.54 0.53 0.52 0.52 0.43
   Win. t 0.57 0.56 0.48 0.44 0.55 0.57 0.57 0.42 0.61 0.61 0.60 0.59 0.58 0.54
   Reg. t 0.52 0.53 0.44 0.44 0.51 0.53 0.56 0.37 0.57 0.57 0.57 0.56 0.56 0.52
  Scaled Student 0.45 0.45 0.48 0.37 0.45 0.47 0.40 0.39 0.41 0.45 0.43 0.46 0.41 0.42
   Win. t 0.56 0.56 0.58 0.47 0.55 0.58 0.49 0.47 0.50 0.56 0.53 0.57 0.50 0.56
   Reg. t 0.51 0.50 0.55 0.46 0.51 0.55 0.46 0.43 0.46 0.53 0.50 0.54 0.47 0.54
Median Raw Student 0.46 0.45 0.38 0.30 0.43 0.43 0.40 0.29 0.47 0.45 0.46 0.44 0.44 0.37
   Win. t 0.55 0.53 0.47 0.40 0.52 0.53 0.50 0.37 0.55 0.54 0.55 0.53 0.53 0.49
   Reg. t 0.49 0.49 0.42 0.39 0.48 0.49 0.48 0.31 0.52 0.49 0.52 0.48 0.49 0.46
  Scaled Student 0.43 0.42 0.45 0.34 0.43 0.43 0.34 0.32 0.37 0.41 0.40 0.41 0.36 0.38
   Win. t 0.54 0.54 0.54 0.43 0.53 0.54 0.42 0.41 0.46 0.51 0.50 0.52 0.45 0.50
   Reg. t 0.48 0.48 0.51 0.42 0.48 0.50 0.38 0.35 0.41 0.47 0.45 0.48 0.42 0.48
Median-polish Raw Student 0.59 0.58 0.47 0.42 0.55 0.57 0.52 0.46 0.62 0.65 0.59 0.61 0.57 0.51
   Win. t 0.64 0.63 0.52 0.48 0.60 0.62 0.61 0.50 0.66 0.69 0.64 0.66 0.63 0.61
   Reg. t 0.64 0.64 0.52 0.51 0.61 0.62 0.62 0.51 0.67 0.68 0.64 0.67 0.64 0.61
  Scaled Student 0.53 0.54 0.55 0.43 0.53 0.54 0.40 0.45 0.43 0.52 0.46 0.54 0.44 0.49
   Win. t 0.62 0.63 0.64 0.52 0.61 0.63 0.51 0.55 0.54 0.62 0.58 0.63 0.54 0.62
   Reg. t 0.62 0.62 0.64 0.55 0.62 0.64 0.53 0.56 0.55 0.64 0.59 0.65 0.55 0.64
  1. We compared the results of the differential expression analysis of the Tissue Mixture Study between HG-U133plus2 and Hugene 1.0 ST arrays, using Student t-test, Regularized t-test and Window t-test. Preprocessing was performed with affyILM. For each combination of summarization/analysis steps (rows), and each comparison of mixtures (columns), Pearson's correlation coefficient has been computed on log10(p-values) between both types of arrays. Underlined characters highlight the top 5 correlation coefficients for each column. The best match table provided by Affymetrix has been used to map probesets between the two platforms. Raw/Scaled labels respectively refers to summarization tests performed with/without a scaling step between arrays.