modelEntry {Envisage}R Documentation

Specify a minimum model for step-wise model fitting

Description

This function allows specification of a minimum model for the step-wise model fitting procedure in the Envisage GUI. This can 'force' terms of interest to always be considered in the model for each gene.

Usage

  modelEntry(pData, Mentry, useParams, labParams, MEorINT, glm.formula) 

Arguments

pData An object of class phenoData containing the phenotypic information for the experiment.
Mentry Object of class tkentry containing the model entry field from the Envisage GUI. This is used if the starting model is specified in the GUI.
useParams Character vector containing the variable names to be used in the model fitting procedure.
labParams Output from function labelParams, containing the indices of the labelling parameters for the phenoData object pData.
MEorINT Character string indicating whether to look at main effect terms only ('ME') or main effect and interaction terms ('INT').
glm.formula Object of class formula containing the minimal model for the step-wise model fitting procedure.

Details

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 modelEntry is used to set up the maximum and minimum models for the Envisage step-wise model fitting procedure. This can be done in one of two ways. If using the command line interface to envisage, the model can be explicitly stated in the command line in the form 'X ~ var1 + var2:var3 + etc.'. However, if using the GUI (widget=TRUE), users can specify the model in terms of the variable labels (of the form p1, p2, p3, etc. (e.g. p1+p3+p5:p6). This function processes these values to give the minimum model for the analysis.

modelEntry is an internal function and is not designed to be accessed by users.

Value

A list is returned with the followig slots:

startingModel An object of class formula giving the minimum model for the the step-wise model fitting procedure.
intPos An internal object used to identify the location of interaction terms within the minimum model.

Author(s)

Sam Robson S.C.Robson@warwick.ac.uk

References

Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) Envisage: model-based significance analysis of microarray gene expression data, manuscript in preparation

See Also

For the main Envisage method, see envisage.


[Package Envisage version 1.0-2 Index]