maDB-package {maDB}R Documentation

Package to store and retrieve microarray experiments into/from a database.

Description

The maDB package allows to store microarray experiments (preprocessed expresion values of one-color (Affymetrix) or two-color microarrays along with sample information and annotation) into a database. As database backend a PostgreSQL database is used, where all needed tables are created automatically once the first experiment is stored into a newly created database using the publishToDB method. The database itself consists of a variety of tables, where the microarray data is stored in a relational way, thus allowing to store two-color microarray data and data from one-color (Affymetrix) microarray experiments in the same database. \ Use openMadbVignette to open the documentation (vignette) of the package.

Details

Package: maDB
Type: Package
Version: 1.9.4
Date: 2007-05-23
License: LGPL

The main function to create the database tables and to insert an experiment into the database is publishToDB. Preprocessed expresion values and sample informations of the submitted MadbSet object are stored into the database. The function loadFromDB can be used to fetch a whole microarray experiment, or a subset of an experiment from the databse. Other functions to access just jubsets of expression values are getEDB. \ The web interface madbWeb (written in PHP) to a microarray database generated with the maDB package is accessible at http://madb.i-med.ac.at/madbWeb. \ Additionally the maDB package provides also functions to create graphical visualizations of microarray data like the drawMA function to generate MA (differential expression against average expression) plots, or drawVolcanoPlot to generate volcano plots. In both plots the local point density can be color coded.

Author(s)

Johannes Rainer Maintainer: johannes.rainer@tcri.at

References

http://madb.i-med.ac.at/madbWeb


[Package maDB version 1.10.0 Index]