Effect of training-sample size and classification difficulty on the accuracy of genomic predictors.
BACKGROUND
As part of the MicroArray Quality Control (MAQC)-II project, this analysis examines how the choice of univariate feature-selection methods and classification algorithms may influence the performance of genomic predictors under varying degrees of prediction difficulty represented by three clinically relevant endpoints.


METHODS
We used gene-expression data from 230 breast cancers (grouped into training and independent validation sets), and we examined 40 predictors (five univariate feature-selection methods combined with eight different classifiers) for each of the three endpoints. Their classification performance was estimated on the training set by using two different resampling methods and compared with the accuracy observed in the independent validation set.


RESULTS
A ranking of the three classification problems was obtained, and the performance of 120 models was estimated and assessed on an independent validation set. The bootstrapping estimates were closer to the validation performance than were the cross-validation estimates. The required sample size for each endpoint was estimated, and both gene-level and pathway-level analyses were performed on the obtained models.


CONCLUSIONS
We showed that genomic predictor accuracy is determined largely by an interplay between sample size and classification difficulty. Variations on univariate feature-selection methods and choice of classification algorithm have only a modest impact on predictor performance, and several statistically equally good predictors can be developed for any given classification problem.
Popovici
Vlad
V
Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Génopode Building, Quartier Sorge, Lausanne CH-1015, Switzerland.
Chen
Weijie
W
Gallas
Brandon G
BG
Hatzis
Christos
C
Shi
Weiwei
W
Samuelson
Frank W
FW
Nikolsky
Yuri
Y
Tsyganova
Marina
M
Ishkin
Alex
A
Nikolskaya
Tatiana
T
Hess
Kenneth R
KR
Valero
Vicente
V
Booser
Daniel
D
Delorenzi
Mauro
M
Hortobagyi
Gabriel N
GN
Shi
Leming
L
Symmans
W Fraser
WF
Pusztai
Lajos
L
D000465:Algorithms; D019540:Area Under Curve; D001943:Breast Neoplasms / Q000737:chemistry / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D011960:Receptors, Estrogen / Q000032:analysis; D018401:Sample Size
D011960:Receptors, Estrogen