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 1.4.0

Index]