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 |

`p` |
a numeric vector containing the p-values of the genes. |

`lambda` |
a numeric vector or value specifying the |

`ncs.value` |
a character string. Only used if |

`ncs.weights` |
a numerical vector of the same length as |

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 |

Holger Schwender, [email protected]

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

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
## 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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