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Table 10 Golub cancer data set

From: Identification of differentially expressed genes by means of outlier detection

  

Ns

  

4

193

291

I

ORdensity (A)

90.28

97.22

97.22

 

limma (B)

97.22

97.22

97.22

 

SAM (C)

97.22

97.22

97.22

II

A vs B

1

127

206

 

A vs C

1

130

213

 

B vs C

4

175

265

III

ORdensity

0.5 (0.71)

150.4 (3.89)

241.8 (6.94)

 

limma

0

12.3 (2.26)

4.3 (1.83)

 

SAM

3.3 (0.48)

151.8 (24.18)

220.7 (35.88)

  

Ns

  

403

556

938

I

ORdensity (A)

97.22

97.22

-

 

limma (B)

97.22

97.22

97.22

 

SAM (C)

97.22

-

-

II

A vs B

274

358

-

 

A vs C

280

-

-

 

B vs C

368

-

-

III

ORdensity

334.1 (6.03)

473.3 (9.56)

-

 

limma

029.2 (2.44)

55.5 (3.10)

149.3 (6.36)

 

SAM

316.3 (50.06)

-

-

  1. Results for different number (Ns) of selected genes: 4 with ORdensity strong selection; 193 with limma and Bonferroni; 291 with ORdensity relaxed selection; 403 with SAM; 556 total potential DE genes and 938 with limma and BH. Rows I present the leave-one-out cross-validation correct classification rate. In bold, the results for the genes selected under the standard criteria for ORdensity, limma and SAM procedures; in rows II, number of common selected genes between the ORdensity, limma and SAM approaches; in rows III, mean and standard deviation (in brackets) of the number of genes that for 10 subsamples were always kept selected