expressionByFeature

 An ExpressionSet, containing the normalized expression values

 eSet

 Function to convert the featureNames (e.g. affy IDs) of eSet to the required features (e.g. ORFs)

 If one feature (e.g. ORF) has more than one feature (e.g. affy ID) on the chip, the mean/median over the intensities is taken

method


This function gets the expression of a specified feature (e.g. orf, gene) from an ExpressionSet.


manip

Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.

Benedikt Zacher

Starr

Simple tiling array analysis of Affymetrix ChIP-chip data

expressionByFeature function

An ExpressionSet, containing the normalized expression values

eSet

Function to convert the featureNames (e.g. affy IDs) of eSet to the required features (e.g. ORFs)

If one feature (e.g. ORF) has more than one feature (e.g. affy ID) on the chip, the mean/median over the intensities is taken

This function gets the expression of a specified feature (e.g. orf, gene) from an ExpressionSet.

expressionByFeature: Getting expression value by feature from an ExpressionSet

Description

Usage

Arguments

See Also