sim.preProcessed {snm} | R Documentation |
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.
sim.preProcessed(seed)
seed |
Numeric value used to seed random number generator. |
|
a 25,000 by 50 matrix of simulated data generated according to the description above. |
|
a vector of indices corresponding to the rows in raw.data of the probes unaffected by the biological variable of interest |
|
a model matrix of the biological variable of interest. |
|
a model matrix of the adjustment variables |
|
set to NULL |
Brig Mecham
snm
, sim.doubleChannel
, sim.singleChannel
, sim.refDesign
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")