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Table 3 True positive rates

From: Comparison of small n statistical tests of differential expression applied to microarrays

   t-stat CyberT LPE BRB limma FC median TPR
HGU133A 42 spikes MAS 5.0 4.5 (.76) 1 (.80) 4.5 (.76) 2.5 (.78) 2.5 (.78) 6 (.30) .77
  RMA 6 (.80) 2.5 (.87) 4.5 (.86) 2.5 (.87) 4.5 (.86) 1 (.89) .87
  gcRMA 6 (.78) 2 (.88) 3 (.86) 4.5 (.83) 4.5 (.83) 1.5 (.89) .85
  dChip 4 (.85) 2.5 (.87) 6 (.83) 1 (.88) 2.5 (.87) 5 (.84) .86
  LMGene 6 (.80) 3.5 (.89) 3.5 (.89) 1 (.91) 5 (.88) 2 (.90) .87
  VSN 6 (.79) 3 (.87) 5 (.85) 1 (.89) 3 (.87) 3 (.87) .89
  avg. rank 6 2.5 4.5 1.8 3.4 2.5  
HGU95 12 spikes MAS 5.0 2 (.73) 1 (.80) 3 (.71) 4.5 (.68) 4.5 (.68) 6 (.11) .70
  RMA 5 (.82) 2.5 (.88) 6 (.81) 2.5 (.88) 2.5 (.88) 2.5 (.88) .88
  gcRMA 6 (.85) 2 (.95) 5 (.89) 4 (.91) 3 (.92) 1 (.96) .92
  dChip 5 (.84) 4 (.87) 6 (.66) 2 (.89) 2 (.89) 2 (.89) .88
  LMGene 5.5 (.89) 2.5 (.85) 5.5 (.89) 2.5 (.89) 4 (.88) 1 (.90) .89
  VSN 5 (.73) 4 (.82) 6 (.66) 2 (.85) 3 (.84) 1 (.86) .83
  avg. rank 4.8 2.7 5.3 2.9 3.2 2.3  
cDNA liver vs liver 288 spikes Loess 5 (.93) 4 (.95) 6 (.65) 2.5 (.97) 2.5 (.97) 1 (.98) .96
  Loess(BC) 5 (.95) 2 (.98) 6 (.88) 2 (.98) 2 (.98) 4 (.97) .98
  glog Loess 5 (.88) 3 (.97) 6 (.78) 3 (.97) 3 (.97) 1 (.98) .97
  glog Loess(BC) 5 (.93) 3 (.97) 6 (.91) 3 (.97) 3 (.97) 1 (.98) .97
  VSN 5 (.89) 2.5 (.98) 6 (.70) 2.5 (.98) 2.5 (.98) 2.5 (.98) .98
  avg. rank 5.0 2.9 6 2.6 2.6 1.9  
cDNA liver vs pool 288 spikes Loess 4 (.63) 1 (.84) 6 (.39) 2 (.83) 3 (.82) 5 (.48) .73
  Loess(BC) 2.5 (.17) 1 (.21) 5 (.12) 4 (.16) 2.5 (.17) 6 (.05) .17
  glog Loess 5 (.92)) 1 (.98) 4 (.96) 2.5 (.97) 2.5 (.97) 6 (.18) .97
  glog Loess(BC) 5 (.93) 1 (.98) 2 (.97) 3.5 (.96) 3.5 (.96) 6 (.16) .96
  VSN 4 (.83) 1 (.97) 5 (.67) 2.5 (.92) 2.5 (.92) 6 (.27) .88
  avg. rank 4.1 1.0 4.4 2.9 2.8 5.8  
Simulated 100 spikes Common 6 (.48) 2.5 (.63) 5 (.51) 2.5 (.63) 2.5 (.63) 2.5 (.63) .63
  Local 5 (.26) 4 (.37) 6 (.24) 2 (.69) 1 (.70) 3 (.42) .40
  Inverse Gamma 5 (.54) 2 (.65) 6 (.51) 2 (.65) 2 (.65) 2 (.62) .64
  avg. rank 5.1 2.5 5.1 2.5 2.6 3.2  
  total avg. rank 5.0 2.3 5.1 2.5 2.9 3.1  
  1. Rankings from best to worst (1 to 5) of average true positive rate (TPR) scores of the six tests of differential expression. The average TPR for each score is in parentheses. The LMGene package was used to apply the Loess normalization and glog transformation to the cDNA data. BC indicates that background correction was applied to the data before normalization.