|
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), non-cancerous samples (19)
|
40233 (39746)
|
|
Sørlie
|
High ER expression (55), low ER expression (18)
|
8033 (7734)
|
|
Ye
|
Metastatic (65), non-metastatic (22)
|
8911
|
|
Normalization (No)
|
Description
| |
|
No 0
|
Raw data
| |
|
No 1
|
Print-tip MA-loess, no background correction
| |
|
No 2
|
Print-tip MA-loess, background correction
| |
|
No 3
|
Global MA-loess, no background correction
| |
|
No 4
|
Global MA-loess, background correction
| |
|
Gene selection (G)
|
Fixed parameters
| |
|
T-test
|
Two-sided
| |
|
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 = [2-5]
|
|
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 = nu-scv, cross = 10, nu = 0.2, scaled = FALSE
| |
|
SVM Poly2
|
Support Vector Machine, polynomial kernel, deg 2, type = nu-scv, cross = 10, nu = 0.2, scaled = FALSE
| |
|
SVM Poly3
|
Support Vector Machine, polynomial kernel, deg 3, type = nu-scv, cross = 10, nu = 0.2, scaled = FALSE
| |
|
SVM Rb
|
Support Vector Machine, radial basis kernel, type = nu-scv, cross = 10, nu = 0.2, scaled = FALSE
|
sigma = [2-14, 214]
|
