Estimation of the prior probability

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Description

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

Usage

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

Arguments

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.

Details

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".

Value

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.

Author(s)

Holger Schwender, holger.schw@gmx.de

References

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

See Also

SAM-class,sam,qvalue.cal

Examples

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## 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)

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