EstimatePi0 {BGmix} | R Documentation |
Estimate of the proportion of the variables under the null hypothesis using tail posterior probabilities
EstimatePi0(tpp, pp0, plot = T)
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 |
Use Storey (2002) approach to estimate pi0
estimate of pi0 = proportion of non-differentially expressed genes
Natalia Bochkina
Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics (in press).
TailPP
, FDRplotTailPP
,histTailPP
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)