| SimMVN.IW {SharedHT2} | R Documentation |
SimMVN.IW generates nsim simulation replicates of a
simulated micro-array expression experiment under the Multivariate Normal/
Inverse Wishart model for the purposes of benchmarking the empirical Bayes
Hotelling T-squared test against three other statistics, the standard
Hotelling T-squared test, the empirical Bayes univariate F test and the
standard univariate F test.
SimMVN.IW(nsim, shape = NULL, rate = NULL, theta = NULL, nreps,
Ngenes, effect.size, FDRlist = 0.05 * (1:5), verbose = F,
gradient = F)
nsim |
Number of simulations desired. |
shape |
The shape parameter for the Inverse Wishart distribution |
rate |
The rate parameter matrix, of dimension d by d
where d is the number of experimental groups. |
theta |
Alternatively to specifying shape and rate
above, the user can directly specify the model parameters from which
shape and rate 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. |
FDRlist |
A list of FDR values to use in the BH step down procedure used in summarizing the simulation results. |
verbose |
Doesn't really belong here. Defaults to FALSE, leave it that way or your log file will grow to large |
gradient |
Also doesn't belong here. Defaults to FALSE, leave it that way. |
A list containing the following 5 components:
fdrtbl |
A matrix of dimension length(FDRlist) by 8, with one row
corresponding to each of the expected FDR's given in FDRlist and having columns
ShHT2-TPR, ShHT2-FPR, HT2-TPR, HT2-FPR,
ShUT2-TPR, ShUT2-FPR, UT2-TPR, UT2-FPR, each giving
the average empirical true/false positive rate over the nsim simulations
for the corresponding statistic. |
countstbl |
An Ngenes by 8 matrix. Instead of thresh-holding the
corresponding p-values by the BH stepdown criterion, unique values of the
statistic are treated as candidate threshold values giving at each simulation
rep empirical true/false positive rates for each of the 4 statistics. These
values are averaged over the nsim simulation reps producing an Ngenes
by 8 matrix. |
coef |
An nsim by d*(d+1)/2 + 1 matrix containing the fitted
model coefficients for the Multivariate Normal/Inverse Wishart model. |
coefEV |
An nsim by 2 matrix containing the fitted model coefficients
for the Normal/Inverse Gamma model. |
call |
The original call to SimMVN.IW |
Grant Izmirlian izmirlian@nih.gov
EB.Anova, EBfit, SimAffyDat,
TopGenes, SimNorm.IG, SimMVN.mxIW,
SimOneNorm.IG, SimOneMVN.IW,
SimOneMVN.mxIW
## Not run:
data(SimAffyDat)
fit.SimAffyDat <- EB.Anova(data=SimAffyDat, labels=c("log2.grp"
H0="zero.means", Var.Struct = "general")
SimResults <-
SimMVN.IW(nsim=500, theta=EBfit(fit.SimAffyDat)$coef, Ngenes=12625,
nreps=3, FDRlist = 0.05*(1:5), effect.size = c(rep(4.33, 100),
rep(0, 12625 - 100)))
# Or create a batch file like this
# contents of mysim.R:
library(SharedHT2)
nsim <- 500
nreps <- 3
Ngenes <- 12625
nTP <- 100
effect.size <- c(rep(4.33, nTP), rep(0, Ngenes - nTP)
theta <- EBfit(fit.SimAffyDat)$coef
SimResults <- SimMVN.IW(nsim=nsim, theta = theta, nreps = nreps,
Ngenes = Ngenes, effect.size = effect.size)
# At the command prompt
R CMD BATCH mysim.R mysim.Rout
# nsim=500, Ngenes=12625, nreps=3, with d=2 groups (implicit in the dimension
# of theta) will take just under 3 hours on a pentium 4.
## End(Not run)