pi0.est {siggenes}R Documentation

Estimation of the prior probability


Estimates the prior probability that a gene is not differentially expressed by the natural cubic splines based method of Storey and Tibshirani (2003).


  pi0.est(p, lambda = seq(0, 0.95, 0.05), ncs.value = "max", 
      ncs.weights = NULL)


p a numeric vector containing the p-values of the genes
lambda a numeric vector or value specifying the lambda values used in the estimation of the prior probability
ncs.value a character string. Only used if lambda is a vector. Either "max" or "paper". For details, see Details
ncs.weights a numerical vector of the same length as lambda containing the weights used in the natural cubic spline fit. By default no weights are used


For each value of lambda, pi0(lambda) is computed by the number of p-values p larger than lambda divided by (1-lambda)m, where m is the length of p.

If lambda is a value, pi0(lambda) is the estimate for the prior probabiltity pi0 that a gene is not differentially expressed.

If lambda is a vector, a natural cubic spline h with 3 degrees of freedom is fitted through the data points (lambda,pi0(lambda)), where each point is weighed by ncs.weights. pi0 is estimated by h(v), where v=max{lambda} if ncs.value="max", and v=1 if ncs.value="paper".


p0 the estimate of the prior probability that a gene is not differentially expressed
spline.out the output of smooth.spline used in this function


Holger Schwender, holger.schw@gmx.de


Storey, J.D., and Tibshirani, R. (2003). Statistical Significance for Genome-wide Studies. PNAS, 100, 9440-9445.

See Also



## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in multtest.

  # Perform a SAM analysis.

  # Estimate the prior probability that a gene is not significant
## End(Not run)

[Package siggenes version 1.4.0 Index]