Calculate PPA significance threshold leading to a desired false discovery rate

Description

In the context of multiple testing and discoveries, a popular approach is to use a common threshold leading to a desired false discovery rate (FDR). In the Bayesian paradigm, derivation of the PPA threshold is trivial and can be calculated using a direct posterior probability calculation as described in Newton et al. (2004).

Usage

calculateThreshold(prob, threshold)

Arguments

Value

References

Newton, MA., Noueiry, A., Sarkar, D. and Ahlquist, P. (2004): "Detecting differential gene expression with a semiparametric hierarchical mixture method."Biometrics, 5(2), 155-176

Examples

data(PPA.liver)
cutoff.liver <- calculateThreshold(PPA.liver, 0.2)

Results

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> library(iBMQ)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/iBMQ/calculateThreshold.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateThreshold
> ### Title: Calculate PPA significance threshold leading to a desired false
> ###   discovery rate
> ### Aliases: calculateThreshold
> 
> ### ** Examples
> 
> data(PPA.liver)
> cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>