MADE4: Multivariate analysis of microarray data using ADE4

What is MADE4?
MADE4 is a package written in the statistical language R. MADE4 enables the multivariate analysis of microarray and other genomic datasets. It can read Bioconductor microarray data formats and send these to the multivariate statistical analysis package ADE4. It has several enhanced graphical functions that aid in the visualisation of results of multivariate analyses of microarray data.

What functions are in MADE4?
A list of the functions in MADE4 and examples of these, are available, see the help pages. A tutorial showing how to apply MADE4 functions is described in the package vignette.

What is the current version of MADE4?
Current version: 1.2.0
Release date: 21st Sept 2005

The most up to date version of MADE4 is available from Bioconductor.

How can I install MADE4?
MADE4 is available in Bioconductor. Download from bioconductor.

MADE4 can be installed using the R commands:

install.packages("made4", repos = "")
Alernatively, Download from bioconductor. and manually install using:
Windows users may download the .zip file, and install using the menu. To do this, click
Packages -> Install package(s) from local zip files
Alternatively, you wish to install from the source (Linux, Mac, or Windows), download the .tar.gz version. At a command prompt type
R CMD install made4_xxx.tar.gz
where xxx is the version number of MADE4.

How do I cite MADE4?
Please cite: Culhane AC, Thioulouse J, Perriere G, Higgins DG. (2005) MADE4: An R package for Multivariate Analysis of Gene Expression Data.Bioinformatics. 21(11): 2789-90. preprint

Where can I download the full example datasets?
Within made4, the example datasets (NCI60, Khan) are reduced. This is to kept the package small. Therefore the Khan dataset only contains 306 of the 2308 genes in this dataset. The NCI60 Ross et al.., and Staunton et al., data only contains 144 rows (genes). The full datasets can be downloaded from

Who do I report bugs to?
If possible please use the R command traceback to get bug info and email this and details of bug to:
[mail address]

Selected images generated using MADE4

between.graph commonMap do3d heatplot.bga
heatplot.bga.jpg html3d html3d_b plot.bga
plot.cia plot.coa rotate3d