title: Merging microarray data, robust feature selection, and predicting prognosis in prostate cancer.
abstract: BACKGROUND
  Individual microarray studies searching for prognostic biomarkers often have few samples and low statistical power; however, publicly accessible data sets make it possible to combine data across studies.
  
  
  METHODS
  We present a novel approach for combining microarray data across institutions and platforms. We introduce a new algorithm, robust greedy feature selection (RGFS), to select predictive genes.
  
  
  RESULTS
  We combined two prostate cancer microarray data sets, confirmed the appropriateness of the approach with the Kolmogorov-Smirnov goodness-of-fit test, and built several predictive models. The best logistic regression model with stepwise forward selection used 7 genes and had a misclassification rate of 31%. Models that combined LDA with different feature selection algorithms had misclassification rates between 19% and 33%, and the sets of genes in the models varied substantially during cross-validation. When we combined RGFS with LDA, the best model used two genes and had a misclassification rate of 15%.
  
  
  BACKGROUND
  Affymetrix U95Av2 array data are available at http://www.broad.mit.edu/cgi-bin/cancer/datasets.cgi. The cDNA microarray data are available through the Stanford Microarray Database (http://cmgm.stanford.edu/pbrown/). GeneLink software is freely available at http://bioinformatics.mdanderson.org/GeneLink/. DNA-Chip Analyzer software is publicly available at http://biosun1.harvard.edu/complab/dchip/.
authors.affiliation: Department of Biostatistics and Applied Mathematics, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA. jingwang@mdanderson.org
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Kim Anh
authors.initials: KA
authors.lastname: Do
authors.forename: Sijin
authors.initials: S
authors.lastname: Wen
authors.forename: Spyros
authors.initials: S
authors.lastname: Tsavachidis
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: McDonnell
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Logothetis
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Coombes