result.output {Envisage} | R Documentation |
This function takes the adjusted p-values for the model terms for each gene and outputs those genes that are significant to the user.
result.output(adjp, pCutoff, pData, exprData, errorGenes, fileResults, MEorINT, param4INT, failedAnova)
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. |
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.
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. |
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
.