FDRplotTailPP {BGmix} | R Documentation |
Plots smoothed FDR vs tail posterior probability or vs the number of differentially expressed (DE) genes
FDRplotTailPP(tpp.res, nmax = sum(! is.na(tpp.res$FDR)), plot.TP = F)
tpp.res |
output of TailPP |
nmax |
maximum size of the list of DE genes |
plot.TP |
logical. If TRUE FDR is plotted, otherwise the number of false positives is plotted vs the number of differentially expressed genes |
Natalia Bochkina
Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics.
TailPP
, histTailPP
,EstimatePi0
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) FDRplotTailPP(tpp.res, plot.TP = TRUE)