plotMA

 	an ExprssionSet or matrix, containing the data 

 eSet 

 an integer, or boolean vector, that indicates, which columns in the ExpressionSet are IP experiments  

 ip 

 an integer, or boolean vector, that indicates, which columns in the ExpressionSet are CONTROL or REFERENCE experiments 

 control 


A matrix of M vs. A plots of each pair (ip, control) is produced.


hplot

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

plotMA function

an ExprssionSet or matrix, containing the data

eSet

an integer, or boolean vector, that indicates, which columns in the ExpressionSet are IP experiments

an integer, or boolean vector, that indicates, which columns in the ExpressionSet are CONTROL or REFERENCE experiments

control

A matrix of M vs. A plots of each pair (ip, control) is produced.

plotMA: M versus A plot

Description

Usage

Arguments

See Also

Examples