result.output {Envisage} | R Documentation

## Output significant genes for package Envisage

### Description

This function takes the adjusted p-values for the model terms for each gene and outputs those genes that are significant to the user.

### Usage

      result.output(adjp, pCutoff, pData, exprData, errorGenes,
        fileResults, MEorINT, param4INT, failedAnova)

### Arguments

`adjp` | An object of class `data.frame` containing the adjusted p-values for each model term for each gene.
`pCutoff` | A number defining the p value cutoff to be used in significance analysis. Must be between 0 and 1 (default 0.05.)
`pData` | An object of class `phenoData` containing the phenotypic information for the experiment.
`exprData` | A matrix of expression values for each gene for each sample. Usually calculated using `exprs` on an object of class `ExpressionSet`.
`errorGenes` | A list of the genes that failed and the model terms for which aliasing was detected.
`fileResults` | The folder in which to save the results of the modelling procedure. Defaults to the current working directory.
`MEorINT` | Character string defining whether to look at first order interactions ("INT") or only main effect terms ("ME") in the model.
`param4INT` | A character vector that defines the model variables for which interactions should be calculated.
`failedAnova` | A vector of genes for which the Anova Type II sum of squares failed, indicating model aliasing.

### 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 `result.output` outputs significant gene lists for each of the terms within the model. For each model term, a vector is created containing any genes for which the adjusted p-value for that terms is below `pCutoff` (along with the corresponding adjusted p-value). A list, `results`, is created containing all such data frames for all model terms.

The resulting p-values for each model term are output in a tab delimitted text file within the directory ‘EnvisageResults/’ which is created within the directory specified by `fileResults` (defaults to the working directory). If this directory already exists, existing files are appended with the suffix ‘OLD’ to distingiush them from the most recent files. This avoids overwriting data, but please be aware that continually writing to the same file will result in an increase in the directory size.

Also created are two output files pertaining to aliasing information. ‘AliasGenes.txt’ gives the names of the genes that show problems due to model aliasing, and ‘AliasReport.txt’ gives a more in depth report on the variable levels for which aliasing was detected. For more information, please see the package vignette.

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

### Value

A list `results` is returned containing the following slots:

`model term` | For each model term, significnat genes and their p-values are comntained within individual slots.
`AliasGenes` | A vector of genes which showed problems through the modelling procedure due to aliasing in the 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]