selectmodel: Select Appropriate Linear Model

In limma: Linear Models for Microarray Data

Description

Select the best fitting linear model for each gene by minimizing an information criterion.

Usage

selectModel(y, designlist, criterion="aic", df.prior=0, s2.prior=NULL, s2.true=NULL, ...)

Arguments

y	a matrix-like data object, containing log-ratios or log-values of expression for a series of microarrays. Any object class which can be coerced to matrix is acceptable including numeric, matrix, MAList, marrayNorm, ExpressionSet or PLMset.
designlist	list of design matrices
criterion	information criterion to be used for model selection, "aic", "bic" or "mallowscp".
df.prior	prior degrees of freedom for residual variances. See squeezeVar
s2.prior	prior value for residual variances, to be used if df.prior>0.
s2.true	numeric vector of true variances, to be used if criterion="mallowscp".
...	other optional arguments to be passed to lmFit

Details

This function chooses, for each probe, the best fitting model out of a set of alternative models represented by a list of design matrices. Selection is by Akaike's Information Criterion (AIC), Bayesian Information Criterion (BIC) or by Mallow's Cp.

The criteria have been generalized slightly to accommodate an information prior on the variances represented by s2.prior and df.prior or by s2.post. Suitable values for these parameters can be estimated using squeezeVar.

Value

List with components

IC	matrix of information criterion scores, rows for probes and columns for models
pref	factor indicating the model with best (lowest) information criterion score

Author(s)

Alicia Oshlack and Gordon Smyth

See Also

An overview of linear model functions in limma is given by 06.LinearModels.

Examples

nprobes <- 100
narrays <- 5
y <- matrix(rnorm(nprobes*narrays),nprobes,narrays)
A <- c(0,0,1,1,1)
B <- c(0,1,0,1,1)
designlist <- list(
  None=cbind(Int=c(1,1,1,1,1)),
  A=cbind(Int=1,A=A),
  B=cbind(Int=1,B=B),
  Both=cbind(Int=1,AB=A*B),
  Add=cbind(Int=1,A=A,B=B),
  Full=cbind(Int=1,A=A,B=B,AB=A*B)
)
out <- selectModel(y,designlist)
table(out$pref)

Example output

None    A    B Both  Add Full 
  23    7    7    3   11   49 

limma documentation built on Nov. 8, 2020, 8:28 p.m.