Alizadeh

DLBCL (68), other samples (65)

7806 (7430)

Finak

Epithelial (34), stromal tissue (32)

33491

Galland

Invasive NFPAs (22), non invasive NFPAs (18)

40475 (40291)

Herschkowitz

High ER expression (58), low ER expression (46)

19718

Jones

Cancerous samples (72), noncancerous samples (19)

40233 (39746)

Sørlie

High ER expression (55), low ER expression (18)

8033 (7734)

Ye

Metastatic (65), nonmetastatic (22)

8911

Normalization (No)

Description
 
No 0

Raw data
 
No 1

Printtip MAloess, no background correction
 
No 2

Printtip MAloess, background correction
 
No 3

Global MAloess, no background correction
 
No 4

Global MAloess, background correction
 
Gene selection (G)

Fixed parameters
 
Ttest

Twosided
 
Relief

Threshold = 0, nosample = # obs. in data set
 
Paired distance

Euclidian distance
 
Number of genes (N)

2, 12, 22, 32, 42, 52, 62, 72, 82, 92, 100, 200, 300, 400, 150, 500, 600, 700, 800, 900, 1000
 
Machine learning (M)

Description, Fixed parameters

Optimized parameters

DT Gini

Decision tree, Splitting index = Gini
 
DT Information

Decision tree, Splitting index = Information
 
NN One layer

Neural Network, one hidden layer, decay = 0.001, rang = 0.1, maxit = 100

size = [25]

NN No layer

Neural Network, no hidden layer, decay = 0.001, rang = 0.1, maxit = 100, skip = TRUE, size = 0
 
SVM Linear

Support Vector Machine, linear kernel, type = nuscv, cross = 10, nu = 0.2, scaled = FALSE
 
SVM Poly2

Support Vector Machine, polynomial kernel, deg 2, type = nuscv, cross = 10, nu = 0.2, scaled = FALSE
 
SVM Poly3

Support Vector Machine, polynomial kernel, deg 3, type = nuscv, cross = 10, nu = 0.2, scaled = FALSE
 
SVM Rb

Support Vector Machine, radial basis kernel, type = nuscv, cross = 10, nu = 0.2, scaled = FALSE

sigma = [2^{14}, 2^{14}]
