dataTransform {Envisage} | R Documentation

## Gene expression data formatting for Envisage

### Description

Ensures that the gene expression data from the `ExpressionSet` object is in the correct format for package Envisage.

### Usage

      dataTransform(expData)

### Arguments

`expData` | Object of class `ExpressionSet` containing gene expression data.

### 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 `dataTransform` is an internal function that ensures that the gene expression data (in the form of an object of class `ExpressionSet`) is in the correct format for future processing. In particular, this function ensures that data is in a logged format.

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

### Value

Returns a matrix of processed expression values (this may be very large).

### 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]