PRABI
Rhone-Alpes Bioinformatics Center


PRABI

ADE4

What is ADE-4 ?

ADE-4 is a multivariate analysis and graphical display software. Multivariate analysis methods available in ADE-4 include usual one-table methods like principal component analysis and correspondence analysis, spatial data analysis methods (using a total variance decomposition into local and global components, analogous to Moran and Geary indices), discriminant analysis and within/between groups analyses, many linear regression methods including lowess and polynomial regression, multiple and PLS (partial least squares) regression and orthogonal regression (principal component regression), projection methods like principal component analysis on instrumental variables, canonical correspondence analysis and many other variants, coinertia analysis and the RLQ method, and several three-way table (k-table) analysis methods. Graphical display techniques include an automatic collection of elementary graphics corresponding to groups of rows or to columns in the data table, thus providing a very efficient way for automatic k-table graphics and geographical mapping options. The user interface is simple and homogeneous among all the programs ; this contributes to make the use of ADE-4 very easy for non specialists in statistics, data analysis or computer science.

The ade4 package is a complete rewrite of the ADE4 software for the R environment. It contains Data Analysis functions to analyse Ecological and Environmental data in the framework of Euclidean Exploratory methods, hence the name ade4 (i.e., 4 is not a version number but means that there are four E in the acronym). The ade4 package is available in CRAN, but it can also be used directly online, thanks to the Rweb system. This possibility is being used to provide multivariate analysis services in the field of bioinformatics, particularly for sequence and genome structure analysis at the PBIL. An example of these services is the automated analysis of the codon usage of a set of DNA sequences by correspondence analysis : COA.

More on ADE-4 ...

Thioulouse J., Chessel D., Dolédec S., & Olivier J.M. (1997) ADE-4 : a multivariate analysis and graphical display software. Statistics and Computing, 7, 1, 75-83

Chessel D., Dufour A.B., & Thioulouse J. (2004). The ade4 package - I : One-table methods. Rnews, 4, 5-10.