public List<String> find() throws IOException {
    //		Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS", "NRAS", "KRAS"));
    //		Set<String> g2 = new HashSet<String>(Arrays.asList("BRAF"));

    Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS"));
    Set<String> g2 = new HashSet<String>(Arrays.asList("NRAS", "KRAS"));

    Map<String, Double> pvals = calcDifferencePvals(g1, g2);

    System.out.println("pvals.size() = " + pvals.size());

    List<String> list = FDR.select(pvals, null, fdrThr);
    System.out.println("result size = " + list.size());

    Map<String, Boolean> dirs = getChangeDirections(list, g1, g2);

    int up = 0;
    int dw = 0;

    for (String gene : dirs.keySet()) {
      Boolean d = dirs.get(gene);
      if (d) up++;
      else dw++;
    }

    System.out.println("up = " + up);
    System.out.println("dw = " + dw);

    return list;
  }
  private double[] toDoubleArray(Map<String, Double> map) {
    double[] d = new double[map.size()];

    int i = 0;
    for (String key : map.keySet()) {
      d[i++] = map.get(key);
    }
    return d;
  }
 private void printResults(Map<String, Double> pvals, List<String> list) {
   for (String s : list) {
     System.out.println(
         s
             + "\t"
             + FormatUtil.roundToSignificantDigits(pvals.get(s), 2)
             + "\t"
             + affectedDw.get(s));
   }
 }