qvalue2: qvalue2
In drmjc/mjcstats: MJC's general statistics library

Description Usage Arguments Details Value Author(s) References Examples

Estimate the q-values for a given set of p-values, in a safe manner. The most frequent error that I have seen in using qvalue, is that pertaining to the “pi_0 estimate is less than zero” which is thrown as a result of not being able to estimate the lambda parameter. This function first attempts to generate qvalues using the default “smoother” method. If that fails due to pi_0 estimate, then this is repeated using the “bootstrap” method. If the same error is still thrown, then a fallback FDR estimation method is used, which defaults to “BH”, the Benjamini-Hochberg FDR

1 2	qvalue2(p, lambda = seq(0, 0.9, 0.05), fallback = c("BH", "fdr", "BY")[1])

`p`	a vector of p-values
`lambda`	The value of the tuning parameter to estimate pi_0. Must be in [0,1). Optional, see Storey (2002).
`fallback`	The fallback p.adjust method. Default = “BH”, but can be one of the other FDR methods from `p.adjust.methods`

In addition, when running library(qvalue) in a headless server, you often get a warning: In fun(libname, pkgname) : no DISPLAY variable so Tk is not available which is actually thrown by tcltk. qvalue2 suppresses that message. See references.

An object of class qvalue, even if the the FDR was estimated using the fallback option, where the latter has pi0=1.0.

Mark Cowley, 2011-10-25

http://stackoverflow.com/a/11554019/178297

p <- runif(100,0,1)
qvalue2(p)
# qv
pbad <- c( 2e-04, 3e-04, 5e-04, 6e-04, 8e-04, 8e-04, 9e-04, 9e-04, 0.001,
           0.001, 0.0013, 0.0013, 0.0013, 0.0014, 0.0016, 0.0017, 0.0019,
           0.0019, 0.0023, 0.0023, 0.0023, 0.0024, 0.0028, 0.0029, 0.0031,
           0.0032, 0.0032, 0.0032, 0.0034, 0.0034, 0.0035, 0.0037, 0.0038,
           0.0038, 0.0042, 0.0043, 0.0044, 0.0044, 0.0044, 0.0045 )
qvalue2(pbad)
# These will now throw errors:
## Not run: 
  qvalue2(p=c(-0.1,0,0.5,0.9,1.0))
  qvalue2(p, lambda=seq(-0.1,1,0.05))
  qvalue2(p, lambda=c(0,0.2,0.5))

## End(Not run)