BGmix (version 1.32.0)

FDRplotTailPP: Plot of FDR for tail posterior probability

Description

Plots smoothed FDR vs tail posterior probability or vs the number of differentially expressed (DE) genes

Usage

FDRplotTailPP(tpp.res, nmax = sum(! is.na(tpp.res$FDR)), plot.TP = F)

Arguments

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

References

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

See Also

TailPP, histTailPP,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)
 FDRplotTailPP(tpp.res, plot.TP = TRUE)