sample.genes.ind: Sample Observations (gene expressions) from Independent...

In warnes/exp.ssize: Estimate Effectivenes of Microarry Sample Size Estimation via Simulation

Description

Sample observations (gene expressions) from independent normal distribution for both control group and the treatment group with known sd for control group and the variance ratio between treatment/control groups.

Usage

sample.genes.ind(ngenes.ind, n, sd.ctrl, var.ratio, delta, distrn = "normal")

Arguments

ngenes.ind	positive integer number of genes to sample the expression
n	positive integer number of replicates for each gene each group (control/treatment)
sd.ctrl	vector of positive numbers for the sample length as ngenes.ind
var.ratio	a positive number for the ratio of variance between treatment and control
delta	effect size for sample size calculation the minimum distance from zero for expression values of genes coming from the true alternative hypothesis group
distrn	distribution of expression data, set to be normal for here

Value

returns a matrix with ngenes.ind rows and 2*n columns with the first n columns being samples from control group and last n columns being from treatment group for each gene (row)

Author(s)

Peng Liu peng\[e-mail]

Examples

##---- Should be DIRECTLY executable !! ----

n.ind <- 100; n <- 500; sd.ctrl <- c(1:100)*0.01
var.ratio1 <- 10;
delta <- 50;

test.sample1 <- sample.genes.ind(n.ind, n, sd.ctrl, var.ratio1, delta)
ndim <- dim(test.sample1);
var.r <- rep(0, ndim[1])
k <- ceiling(n.ind * runif(1,0,1))

for ( i in c(1:ndim[1]))
  { var.r[i] <- var(test.sample1[i,(n+1):(2*n)]) / var(test.sample1[i,1:n])}

cat("comparison between the desired sample and the generated sample: \n")

cat(" ------------------------------------------ \n",
    "number of genes (rows) :\t", n.ind, "\t", ndim[1], "\n",
    "number of obs for each group: \t", n, "\t", ndim[2]/2, "\n",
    "variance ratio (trt/ctrl) is: \t", var.ratio1, "\t", mean(var.r), "\n",
    "sd for gene", k, ":\t\t", sd.ctrl[k], "\t", sd(test.sample1[k,1:n]), "\n",
    "------------------------------------------ \n")

warnes/exp.ssize documentation built on May 4, 2019, 12:59 a.m.