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Table 7 Comparison of the differential expression analysis between HG-U133Plus2 and Hugene 1.0 ST arrays preprocessed with several popular algorithms

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

Method 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
MAS 5 1-Step Tukey-Biweight PM Student 0.51 0.49 0.46 0.36 0.48 0.52 0.49 0.40 0.52 0.55 0.54 0.56 0.49 0.45
   Win. t 0.60 0.57 0.54 0.46 0.56 0.62 0.59 0.48 0.61 0.63 0.63 0.64 0.58 0.58
   Reg. t 0.54 0.52 0.49 0.46 0.52 0.58 0.56 0.42 0.57 0.60 0.59 0.60 0.55 0.54
  PM Student 0.48 0.49 0.49 0.42 0.50 0.50 0.44 0.40 0.44 0.46 0.48 0.47 0.45 0.49
  Norm Win. t 0.57 0.57 0.59 0.53 0.59 0.61 0.55 0.51 0.55 0.57 0.58 0.58 0.55 0.60
   Reg. t 0.50 0.51 0.56 0.53 0.54 0.58 0.52 0.47 0.52 0.55 0.55 0.56 0.49 0.59
Plier Raw Student 0.51 0.59 0.48 0.41 0.52 0.49 0.40 0.43 0.57 0.59 0.56 0.56 0.46 0.49
   Win. t 0.58 0.64 0.54 0.49 0.59 0.58 0.52 0.51 0.62 0.64 0.62 0.62 0.56 0.60
   Reg. t 0.56 0.64 0.54 0.52 0.58 0.58 0.52 0.51 0.61 0.65 0.60 0.62 0.55 0.60
dChip Li-Wong MBEI PM Student 0.46 0.49 0.41 0.43 0.48 0.47 0.41 0.36 0.31 0.44 0.41 0.49 0.40 0.49
  Norm Win. t 0.54 0.55 0.49 0.51 0.55 0.56 0.50 0.47 0.39 0.52 0.50 0.58 0.47 0.58
   Reg. t 0.48 0.51 0.45 0.51 0.53 0.52 0.46 0.41 0.30 0.49 0.45 0.55 0.41 0.55
RMA Median-polish Norm Student 0.54 0.55 0.55 0.46 0.52 0.54 0.44 0.46 0.45 0.52 0.48 0.52 0.49 0.52
   Win. t 0.64 0.64 0.64 0.56 0.62 0.65 0.56 0.58 0.57 0.64 0.59 0.63 0.59 0.64
   Reg. t 0.65 0.66 0.66 0.60 0.64 0.66 0.58 0.60 0.59 0.67 0.62 0.65 0.61 0.67
GCRMA Median-polish Raw Student 0.58 0.61 0.57 0.46 0.52 0.60 0.43 0.60 0.49 0.63 0.54 0.65 0.48 0.57
   Win. t 0.63 0.64 0.59 0.49 0.56 0.64 0.49 0.64 0.54 0.67 0.61 0.68 0.54 0.63
   Reg. t 0.63 0.65 0.60 0.52 0.56 0.65 0.52 0.65 0.52 0.68 0.62 0.69 0.52 0.64
  Norm Student 0.50 0.49 0.48 0.46 0.49 0.51 0.47 0.51 0.47 0.50 0.48 0.51 0.47 0.49
   Win. t 0.60 0.59 0.59 0.55 0.57 0.61 0.54 0.60 0.56 0.61 0.58 0.60 0.56 0.61
   Reg. t 0.59 0.61 0.61 0.59 0.59 0.62 0.56 0.63 0.58 0.64 0.60 0.63 0.57 0.62
  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 several popular methods. For each combination of preprocessing/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/Norm labels refer to raw and normalized data, PM stands for PM-only methods.