| SimOneMVN.IW {SharedHT2} | R Documentation |
SimOneMVN.IW generates a single simulated micro-array expression
experiment under the Multivariate Normal/Inverse Wishart model. This can be used
to generate a variety of example datasets.
SimOneMVN.IW(shape = NULL, rate = NULL, theta = NULL, nreps, Ngenes,
effect.size)
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. |
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.
Grant Izmirlian izmirlian@nih.gov
EB.Anova, EBfit, SimAffyDat,
TopGenes, SimNorm.IG, SimMVN.IW,
SimMVN.mxIW, SimOneNorm.IG,
SimOneMVN.mxIW
## Not run:
shape <- 9.107182
rate <- matrix(c(0.12789434, 0.08468535, 0.08468535, 0.12390469), 2, 2)
Ngenes <- 12625
nreps <- 3
nTP <- 100
effect.size <- c(rep(4.33, nTP), rep(0, Ngenes-nTP))
MyDat <- SimOneMVN.IW(shape=shape, rate=rate, Ngenes=Ngenes, nreps=nreps,
effect.size=effect.size)
# 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)
## End(Not run)