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Table 3 Overlap R(A, B) between sets of genes marked as differentially expressed after pre-processing with different methods. p- and q-values for the significance of difference in expression between samples from the AML dataset with recurrent FLT3 mutation and samples without recurrent FLT3 mutation were calculated. The numbers on the diagonal represents the number of probe sets marked as differentially expressed after application of each method.

From: The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

   MAS dChip RMA GCRMA
SAM q-values MAS 3185    
  dChip 0.68 2973   
  RMA 0.72 0.72 3649  
  GCRMA 0.73 0.70 0.86 3650
t-test p-values MAS 458    
  dChip 0.66 354   
  RMA 0.68 0.70 419  
  GCRMA 0.69 0.71 0.83 472
Wilcoxon test p-values MAS 337    
  dChip 0.72 295   
  RMA 0.75 0.79 322  
  GCRMA 0.75 0.79 0.87 344