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Bioinformatics Advance Access published online on March 29, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti394
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 9, 2005
Revised March 16, 2005
Accepted March 16, 2005

Applications note

MADE4: an R package for multivariate analysis of gene expression data

Aedín C. Culhane 1*, Jean Thioulouse 2, Guy Perrière 2, and Desmond G. Higgins 1

1 Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland
2 Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard - Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France


  Abstract

Summary: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene expression data. MADE4 accepts a wide variety of gene expression data formats. MADE4 takes advantage of the extensive multivariate statistical and graphical functions in the R package ade4, extending these for application to microarray data. In addition MADE4 provides new graphical and visualisation tools that aid in interpretation of multivariate analysis of microarray data.

Availability: The R package MADE4 is available from Bioconductor www.bioconductor.org and bioinf.ucd.ie/software/.

Supplementary information: MADE4 is well documented. There are tutorials, in the form of vignettes, which describe typical analyses. In addition the MADE4 manual provides descriptions and examples for each function.


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