madsim (version 1.2.1)

madsim-package: A Flexible Microarray Data Simulation Model

Description

madsim allows to generate two conditions biological synthetic microarray dataset whith known characteristics. These data have similar behavior as those obtained with current microarray platforms.

Details

Package:

madsim

Type:

Package

Version:

1.2.1

Date:

2016-12-07

License:

GPL (>=2.0)

This package has only one function

References

Dembele D. (2013), A Flexible Microarray Data Simulation Model, Microarrays, 2013, 2(2):115-130

Examples

# set parameters settings
fparams <- data.frame(m1 = 7, m2 = 7, shape2 = 4, lb = 4, ub = 14, pde = 0.02, sym = 0.5);
dparams <- data.frame(lambda1 = 0.13, lambda2 = 2, muminde = 1, sdde = 0.5);
sdn <- 0.4; rseed <- 50;

# generate synthetic data without using real microarray data as seed
mydata <- madsim(mdata=NULL, n=10000, ratio=0, fparams, dparams, sdn, rseed);

# calculate MMplot variables using samples 1 and 12
A <- 0.5*(mydata$xdata[,12] + mydata$xdata[,1]);
M <- mydata$xdata[,12] - mydata$xdata[,1];

# draw MA plot using samples 1 and 12
plot(A,M)