normalize.ExpressionSet.nordi: normal discretization normalization

In virtualArray: Build virtual array from different microarray platforms

Description

Performs a discretization of continous expression levels to discrete steps.

Usage

normalize.ExpressionSet.nordi(ExpressionSet = NULL, pvalue = 0.01, alpha = 0.05, ...)

Arguments

ExpressionSet	An ExpressionSet object
pvalue	The pvalue determines the sensitivity for detecting outliers in each column of the gene expression matrix.
alpha	The alpha value determines the size of the tails of the normal distributions considered to be over or under expressed.
...	Can be used to pass on parameters to underlying functions.

Details

Please see the references for details.

Value

An ExpressionSet object with adjusted expression matrix.

Author(s)

Andreas Heider

References

"GenMiner: Mining informative association rules from genomic data." Ricardo Martinez, Claude Pasquier and Nicolas Pasquier, Proceedings of the IEEE BIBM international conference on Bioinformatics and Biomedecine, pages 15-22, IEEE Computer Society, 2007.

Martinez R, Pasquier N, Pasquier C: GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. Bioinformatics 2008, 24:2643-2644.

See Also

virtualArrayExpressionSets

Examples

# library(affydata)
# data(Dilution)
# Dilution <- rma(Dilution)
# normalize.ExpressionSet.nordi(Dilution)

virtualArray documentation built on Sept. 12, 2016, 6:10 a.m.