alias.glmNA {Envisage} | R Documentation |
Find aliases (linearly dependent terms) in a linear model
specified by a formula. This extends the S3 method
alias
to objects of class
glmNA
for package Envisage.
## S3 method for class 'glmNA': alias(object, ...)
object |
A fitted model object of class
glmNA . |
... |
Further arguments passed to or from other methods. |
The Envisage package contains methods allowing the use of linear models (LMs) for analysing significantly changing genes in experiments with a variety of sources of variation, be they experimentally controlled variables such as drug treatment or time, or non-controlled sources of confounding variation such as phenotypic or environmental differences. This allows all sources of variation to be considered when analysing for significant differential expression, ensuring resulting genes are biologically relevent to the experimental question.
The function alias.glmNA
extends the method
alias
to the S4 class
glmNA
for package
Envisage. This is an extension of classes glm
and
lm
and deals appropriately with genes that produce NA calls in
the modelling procedure. This allows use of the function
Anova
for calculating significance for each gene.
alias.glmNA
is an internal function and is not
designed to be accessed by users.
A list (of class "listof") containing components:
Model |
Description of the model; usually the formula. |
Complete |
A matrix with columns corresponding to effects that are linearly dependent on the rows. |
Partial |
The correlations of the estimable effects, with a zero diagonal. An object of class "mtable" which has its own print method. |
Sam Robson S.C.Robson@warwick.ac.uk
Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) Envisage: model-based significance analysis of microarray gene expression data, manuscript in preparation.
coef
, glmNA. For the main \pkg{Envisage} method, see
\code{envisage}.