pi0.est {siggenes} | R Documentation

## Estimation of the prior probability

### 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

      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

    ## 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)

[Package siggenes version 1.64.0 Index]