convest {limma} | R Documentation |

## Estimate Proportion of True Null Hypotheses

### Description

Returns an estimate of the proportion of true null hypotheses using a convex decreasing density estimate on a vector of
p-values.

### Usage

convest(p, niter = 100, doplot = FALSE, doreport = FALSE)

### Arguments

`p` |
numeric vector of p-values, calculated using any test of your
choice. Missing values are not allowed |

`niter` |
number of iterations to be used in fitting the convex,
decreasing density for the p-values. Default is 100. |

`doplot` |
logical, should updated plots of fitted convex decreasing
p-value density be produced at each iteration?
Default is `FALSE` . |

`doreport` |
logical, should the estimated proportion be printed at each iteration?
Default is `FALSE` . |

### Details

The proportion of true null hypotheses is often denoted pi0.

### Value

Numeric value in the interval [0,1] representing he estimated proportion of true null hypotheses.

### Author(s)

Egil Ferkingstad and Mette Langaas

### References

Egil Ferkingstad, Mette Langaas and Bo
Lindqvist (2003). Estimating the proportion of true null hypotheses, with application
to DNA microarray data. Preprint Statistics No. 4/2003, Department of Mathematical Sciences, Norwegian University
of Science and Technology.
http://www.math.ntnu.no/~mettela/SFG/research.imf

### See Also

See 08.Tests for other functions for producing or interpretting p-values.

### Examples

# First simulate data, use no.genes genes and no.ind individuals,
# with given value of pi0. Draw from normal distribution with mean=0
# (true null) and mean=mean.diff (false null).
no.genes <- 1000
no.ind <- 20
pi0 <- 0.9
mean.diff <- 1
n1 <- round(pi0*no.ind*no.genes)
n2 <- round((1-pi0)*no.ind*no.genes)
x <- matrix(c(rnorm(n1,mean=0),rnorm(n2,mean=mean.diff)),ncol=no.ind,byrow=TRUE)
# calculate p-values using your favorite method, e.g.
pvals <- ebayes(lm.series(x))$p.value
# run the convex decreasing density estimator to estimate pi0
convest(pvals,niter=100,doplot=interactive())

[Package

*limma* version 2.4.7

Index]