pi0.est: Estimation of the prior probability
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	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.

SAM-class,sam,qvalue.cal

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

  # Perform a SAM analysis.
  sam.out<-sam(golub, golub.cl, B=100, rand=123)

  # Estimate the prior probability that a gene is not significant
  pi0.est(sam.out@p.value)

## End(Not run)