EstimatePi0

0th

Percentile

Proportion of the variables under the null hypothesis

Estimate of the proportion of the variables under the null hypothesis using tail posterior probabilities

Keywords
htest
Usage
EstimatePi0(tpp, pp0, plot = T)
Arguments
tpp
observed tail posterior probability
pp0
a vector of tail posterior probability under H0
plot
if True, estimated pi0 at different locations and the median estimate is plotted
Details

Use Storey (2002) approach to estimate pi0

Value

estimate of pi0 = proportion of non-differentially expressed genes

References

Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics (in press).

See Also

TailPP, FDRplotTailPP,histTailPP

Aliases
  • EstimatePi0
Examples

 data(ybar, ss)
 nreps <- c(8,8)

## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
 outdir <- BGmix(ybar, ss, nreps, jstar=-1, nburn=0, niter=100, nthin=1)

 params <- ccParams(outdir)  
 res <-  ccTrace(outdir)
  
 tpp.res <- TailPP(res, nreps, params, plots  = FALSE)
 pi0 <- EstimatePi0(tpp.res$tpp, tpp.res$pp0)

Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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