vsn: sagmbSimulateData – R documentation

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vsn

sagmbSimulateData

Simulate data and assess vsn's parameter estimation

Description

Functions to validate and assess the performance of vsn through simulation of data.

Usage

sagmbSimulateData(n=8064, d=2, de=0, up=0.5, nrstrata=1,  miss=0, log2scale=FALSE)
sagmbAssess(h1, sim)

Arguments

`n`	Numeric. Number of probes (rows).
`d`	Numeric. Number of arrays (columns).
`de`	Numeric. Fraction of differentially expressed genes.
`up`	Numeric. Fraction of up-regulated genes among the differentially expressed genes.
`nrstrata`	Numeric. Number of probe strata.
`miss`	Numeric. Fraction of data points that is randomly sampled and set to `NA`.
`log2scale`	Logical. If `TRUE`, glog on base 2 is used, if `FALSE`, (the default), then base e.
`h1`	Matrix. Calibrated and transformed data, according, e.g., to vsn
`sim`	List. The output of a previous call to `sagmbSimulateData`, see Value

Details

Please see the vignette.

Value

For sagmbSimulateData, a list with four components: hy, an n x d matrix with the true (=simulated) calibrated, transformed data; y, an n x d matrix with the simulated uncalibrated raw data - this is intended to be fed into vsn2; is.de, a logical vector of length n, specifying which probes are simulated to be differentially expressed. strata, a factor of length n.

For sagmbSimulateData, a number: the root mean squared difference between true and estimated transformed data.

Author(s)

Wolfgang Huber

References

Wolfgang Huber, Anja von Heydebreck, Holger Sueltmann, Annemarie Poustka, and Martin Vingron (2003) "Parameter estimation for the calibration and variance stabilization of microarray data", Statistical Applications in Genetics and Molecular Biology: Vol. 2: No. 1, Article 3. http://www.bepress.com/sagmb/vol2/iss1/art3

Examples

sim <- sagmbSimulateData(nrstrata = 4)
  ny  <- vsn2(sim$y, strata = sim$strata)
  res <- sagmbAssess(exprs(ny), sim)
  res

vsn

Variance stabilization and calibration for microarray data

v3.58.0

Artistic-2.0

Authors

Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth

Initial release