snm (version 1.20.0)

sim.preProcessed: Simulate data from a microarray experiment without any intensity-dependent effects.

Description

Simulated data set influenced by a single probe-specific biological and two probe-specific adjustment variables. This parameters for this data are identical to single channel simulated data available as sim.singleChannel(seed) with the difference that this example does not include the intensity-dependent effects. Consult the corresponding help file for details on this simulation.

Usage

sim.preProcessed(seed)

Arguments

seed

Numeric value used to seed random number generator.

Value

raw.data

a 25,000 by 50 matrix of simulated data generated according to the description above.

true.nulls

a vector of indices corresponding to the rows in raw.data of the probes unaffected by the biological variable of interest

bio.var

a model matrix of the biological variable of interest.

adj.var

a model matrix of the adjustment variables

int.var

set to NULL

See Also

snm, sim.doubleChannel, sim.singleChannel, sim.refDesign

Examples

preProcessed <- sim.preProcessed(12347)
snm.obj <- snm(preProcessed$raw.data, 
                      preProcessed$bio.var,
                      preProcessed$adj.var, rm.adj=TRUE)
ks.test(snm.obj$pval[preProcessed$true.nulls],"punif")