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Bioinformatics Advance Access originally published online on March 29, 2005
Bioinformatics 2005 21(11):2789-2790; 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{at}oupjournals.org

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

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

*To whom correspondence should be addressed.

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 visualization tools that aid in interpretation of multivariate analysis of microarray data.

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

Contact: aedin.culhane{at}ucd.ie

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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