maDB

Microarray database and utility functions for microarray data analysis.

Bioconductor version: 2.8

maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays.

Author: Johannes Rainer <johannes.rainer at i-med.ac.at>

Maintainer: Johannes Rainer <johannes.rainer at i-med.ac.at>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("maDB")

To cite this package in a publication, start R and enter:

    citation("maDB")

Documentation

PDF maDB-015.pdf
PDF maDB-016.pdf
PDF maDB.pdf
PDF   Reference Manual

Details

biocViews Microarray, TwoChannel, OneChannel, Visualization
Depends R (>= 2.6.0), Biobase(>= 2.5.5), affy(>= 1.23.4), pgUtils(>= 1.23.2), limma(>= 1.8.0), methods
Imports
Suggests annaffy(>= 1.6.2), biomaRt(>= 1.8.2), geneplotter
System Requirements
License LGPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.24.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source maDB_1.24.0.tar.gz
Windows Binary
MacOS 10.5 (Leopard) binary maDB_1.24.0.tgz
Package Downloads Report Download Stats

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