SimOnenu.mix {SharedHT2}R Documentation

Simulate a micro-array experiment dataset

Description

SimOnenu.mix generates a single simulated micro-array expression experiment under the Wishart/mixed Inverse Wishart model. This can be used to generate a variety of example datasets which violate the assumptions of the Wishart/Inverse Wishart model. See the documentation for Simnu.mix for more details (type ?Simnu.mix).

Usage

  SimOnenu.mix(nu = NULL, Lambda = NULL, theta = NULL, f1f2 = c(1/4, 1/2),
               nreps, Ngenes, effect.size)

Arguments

nu The shape parameter for the Inverse Wishart distribution with equal averaged-over-genes group variance.
Lambda The rate parameter matrix, of dimension d by d where d is the number of experimental groups.
theta Alternatively to specifying nu and Lambda above, the user can directly specify the model parameters from which nu and Lambda are computed. Type ?EBfit for more details.
nreps Number of replicates per group.
Ngenes Number of rows (or genes) in the dataset (micro-array experiment)
effect.size A vector of length Ngenes giving the effect size. Rows with population mean zero (not differentially expressed) are set to zero while rows with non-zero population mean (differentially expressed) are set to some non-zero value. For a feeling of corresponding power in the naive F test of all means identically zero see the documetation on find.ncp by typing ?find.ncp.
f1f2 A vector of length 2 containing strictly increasing values between 0 and 1. These are additional parameters specifying the mixing proportion for the discrete two component mixture and the proportion of the fractional part of nu/(2*d+2) specifying the amount by which one of the two shape parameters should exceed 1. The other shape parameter is derived so that the averaged-over-genes group variances are equal to their values under the corresponding Wishart/Inverse Wishart model.

Value

A dataframe having Ngenes rows and nreps * d columns where d is implicit in the dimension of Lambda, (see above). See the documentation for SimAffyDat for more details.

Author(s)

Grant Izmirlian izmirlian@nih.gov

See Also

EB.Anova, EBfit, SimAffyDat, TopGenes, Simnu.mix

Examples

  nu <- 9.107182
  Lambda <- matrix(c(0.12789434, 0.08468535, 0.08468535, 0.12390469), 2, 2)
  Ngenes <- 12625
  nreps <- 3
  nTP <- 100

  MyDat <- SimOnenu.mix(nu=nu, Lambda=Lambda, Ngenes=Ngenes, nreps=nreps, 
                        effect.size=c(rep(7.5/nreps^{0.5}, nTP), rep(0, Ngenes-nTP)))

# notice the names given to the columns by default:

  names(MyDat)

# Now try out 'EB.Anova' on your dataset

  fit.MyDat <- EB.Anova(data=MyDat, labels= "log2.grp" %,% (1:2), H0="zero.means")

# View the sorted genelist

  TopGenes(fit.MyDat, FDR=0.05, allsig=TRUE)


[Package SharedHT2 version 1.3 Index]