labelParams {Envisage} | R Documentation |
This function removes any categorical variables which have the same number of levels as there are samples (labelling variables).
labelParams(pData)
pData |
An object of class
phenoData containing the
phenotypic information for the experiment. |
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 labelParams
ensures that any
categorical variables included by the user for model fitting that have
the same number of factor levels as there are samples are removed
prior to fitting the model. Such labelling variables contain a unique
value for each sample, and will this result in a perfect fit for the
data.
labelParams
is an internal function and is not
designed to be accessed by users.
A vector is returned containing the indices of the labelling
parameters for the phenoData
object pData
.
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
For the main Envisage method, see envisage
.