FHarray: R package for Finite Hybridization model

History

1. 2008/3/28: Version 0.9.0 Published

Table of Contents

1. Introduction
2. Download
3. Reference

Introduction

The FHarray package is an implementation of expression analysis method using Affymetrix's GeneChip for R software.
The method is based on the Finite Hybridization model, which is an extension of the Langmuir model that predicts signal intensity from the hybridization energy of each probe.
This model considers equilibrium of probe-target duplex formation without assuming excess abundance of neither probe nor target molecules, so that the dynamic range of estimation of expression level is much wider than preceding studies. We also introduced detailed physico-chemical effects such as secondary structure and target-target interaction into the model, in order to improve accuracy and sensitivity of the analysis.
The detail description will be published as an article in Bioinformatics journal (in press).

This packages is developed using affy packages provided by Bioconductor project. We als have submitted this package to Bioconductor .
It will be appear after the review process by the developer committees.

How to install

For UNIX or MacOSX users

1. Download the source package.
2. Open R console, setwd to the directory where the package was placed.
3. Install package by install.packages as follows,

> install.packages(pkgs="FHarray_0.9.0.tar.gz",repos=NULL,type="source")

For Windows XP users

1. Download the binary package for Windows XP.
2. Open R console, setwd to the directory where the package was placed.
3. Install package by install.packages as follows,

> install.packages(pkgs="FHarray_0.9.0.zip",repos=NULL)

Download

• Source package: FHarray_0.9.0.tar.gz
• Binary package for Windows FHarray_0.9.0.zip (compiled by R 2.6.2)

Reference