Table 5 AUC mean values for Simulation study 1, scenario 1 and 100 runs. In first column: n indicates the number of DE gens; Δ the Δ values; A the ORdensity method; B the limma method and C the SAM method

n_X=n_Y=30

n

50

100

Δ

1.5

2

3

1.5

2

3

A

0.998

0.998

0.997

0.998

0.997

0.995

(0.002)

(0.001)

(0.002)

(0.001)

(0.002)

(0.003)

B

0.995

0.993

0.993

0.997

0.993

0.993

(0.002)

(0.000)

(0.000)

(0.003)

(0.000)

(0.000)

C

0.994

0.993

0.993

0.996

0.993

0.993

(0.003)

(0.000)

(0.000)

(0.002)

(0.000)

(0.000)

n_X=n_Y=30

n_X=30, n_Y=10

n

200

50

Δ

1.5

2

3

1.5

2

3

A

0.996

0.997

0.993

0.974

0.996

0.998

(0.000)

(0.000)

(0.000)

(0.001)

(0.001)

(0.001)

B

0.997

0.992

0.992

0.967

0.996

0.993

(0.003)

(0.001)

(0.000)

(0.011)

(0.003)

(0.001)

C

0.998

0.992

0.992

0.940

0.994

0.993

(0.002)

(0.001)

(0.000)

(0.016)

(0.003)

(0.001)

n_X=30, n_Y=10

n

100

200

Δ

1.5

2

3

1.5

2

3

A

0.973

0.994

0.998

0.959

0.992

0.997

(0.001)

(0.002)

(0.003)

(0.000)

(0.000)

(0.000)

B

0.981

0.997

0.993

0.993

0.998

0.992

(0.006)

(0.003)

(0.000)

(0.002)

(0.002)

(0.000)

C

0.946

0.995

0.993

0.960

0.996

0.992

(0.010)

(0.003)

(0.000)

(0.007)

(0.002)

(0.000)

n_X=n_Y=10

n

50

100

Δ

1.5

2

3

1.5

2

3

A

0.925

0.974

0.998

0.921

0.971

0.997

(0.014)

(0.011)

(0.011)

(0.010)

(0.001)

(0.008)

B

0.894

0.980

0.994

0.931

0.989

0.994

(0.023)

(0.009)

(0.001)

(0.013)

(0.004)

(0.002)

C

0.859

0.959

0.994

0.865

0.960

0.994

(0.023)

(0.015)

(0.001)

(0.016)

(0.009)

(0.002)

n_X=n_Y=10

n

200

Δ

1.5

2

3

A

0.900

0.956

0.996

(0.002)

(0.001)

(0.001)

B

0.968

0.996

0.993

(0.007)

(0.001)

(0.003)

C

0.876

0.974

0.995

(0.017)

(0.007)

(0.003)