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Table 2 pAUC scores

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

  

t-stat

CyberT

LPE

BRB

limma

FC

median pAUC

HGU133A

MAS 5.0

5 (.68)

1 (.75)

4 (.69)

2.5 (.70)

2.5 (.70)

6 (.18)

.70

 

RMA

6 (.74)

1.5 (.85)

4.5 (.83)

1.5 (.85)

4.5 (.83)

1 (.84)

.84

 

gcRMA

6 (.74)

1.5 (.85)

3 (.83)

4.5 (.79)

4.5 (.79)

1.5 (.85)

.81

 

dChip

4 (.80)

2 (.83)

5 (.78)

2 (.83)

2 (.83)

6 (.76)

.82

 

LMGene

6 (.75)

2.5 (.85)

2.5 (.85)

1 (.88)

4.5 (.84)

4.5 (.84)

.85

 

VSN

6 (.74)

2.5 (.84)

5 (.82)

1 (.86)

2.5 (.84)

4 (.83)

.84

 

avg. rank

5.5

1.8

4

2.1

2.4

4.2

 

HGU95

MAS 5.0

3 (.59)

1 (.73)

2 (.63)

4.5 (.44)

4.5 (.44)

6 (.10)

.52

 

RMA

6 (.68)

1 (.85)

1.5 (.73)

2.5 (.84)

2.5 (.84)

4 (.83)

.84

 

gcRMA

6 (.76)

1.5 (.91)

5 (.81)

3.5 (.88)

3.5 (.88)

1.5 (.91)

.88

 

dChip

5 (.73)

3 (.82)

6 (.52)

1.5 (.83)

1.5 (.83)

4 (.80)

.81

 

LMGene

5.5 (.74)

1 (.86)

5.5 (.74)

4 (.84)

2.5 (.85)

2.5 (.85)

.85

 

VSN

5.5 (.57)

4 (.76)

5.5 (.57)

2.5 (.80)

2.5 (.80)

1 (.82)

.78

 

avg. rank

5.2

1.9

4.8

3.1

2.8

3.2

 

cDNA liver vs liver

Loess

5 (.78)

4 (.88)

6 (.65)

2.5 (.96)

2.5 (.96)

1 (.97)

.92

 

Loess(BC)

3.5 (.85)

1 (.96)

5 (.80)

3.5 (.85)

2 (.86)

6 (.66)

.85

 

glog Loess

5 (.79)

2 (.96)

6 (.62)

3.5 (.95)

3.5 (.95)

1 (.98)

.95

 

glog Loess(BC)

5 (.81)

1 (.96)

6 (.75)

4 (.93)

3.5 (.93)

3.5 (.94)

.93

 

VSN

5 (.77)

3 (.96)

6 (.61)

3 (.96)

3 (.96)

1 (.97)

.96

 

avg. rank

4.7

2.2

5.8

3.2

2.9

2.2

 

cDNA liver vs pool

Loess

4 (.29)

3 (.39)

6 (.16)

1 (.44)

2 (.43)

5 (.17)

.51

 

Loess(BC)

2.5 (.09)

2.5 (.09)

5 (.05)

2.5 (.09)

2.5 (.09)

6 (.02)

.09

 

glog Loess

4 (.62))

1 (.73)

5 (.56)

2.5 (.69)

2.5 (.69)

6 (.08)

.65

 

glog Loess(BC)

4 (.62)

1 (.73)

5 (.58)

3 (.65)

2 (.66)

6 (.06)

.64

 

VSN

4 (.50)

1 (.57)

5 (.38)

2.5 (.55)

2.5 (.55)

6 (.05)

.53

 

avg. rank

3.7

1.7

5.2

2.3

2.3

5.8

 

Simulated

Common

6 (.32)

4 (.53)

5 (.42)

2 (.54)

2 (.54)

2 (.54)

.54

 

Local

6 (.15)

4 (.27)

5 (.16)

2 (.60)

1 (.61)

3 (.31)

.29

 

Inverse Gamma

5 (.39)

2 (.53)

6 (.35)

2 (.53)

2 (.53)

4 (.48)

.51

 

avg. rank

5.7

3.3

5.3

2.2

1.2

3.3

 
 

total avg. rank

5.0

2.2

5.0

2.6

2.3

3.7

 
  1. Rankings from best to worst (1 to 5) of average pAUC scores (using a threshold of 0.05) of the six tests of differential expression. The average pAUC 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.
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BMC Bioinformatics

ISSN: 1471-2105

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