# Multivariate analysis of microarray data using ADE4

## Documentation for package ‘made4’ version 1.87.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

bet.coinertia | Between class coinertia analysis
between.graph | Plot 1D graph of results from between group analysis
bga | Between group analysis
bga.jackknife | Jackknife between group analysis
bga.suppl | Between group analysis with supplementary data projection
cia | Coinertia analysis: Explore the covariance between two datasets
commonMap | Plot highlights common points between two 1D plots (biparitite)
comparelists | Return the intersect, difference and union between 2 vectors
do3d | Generate 3D graph(s) using scatterplot3d
getcol | Specialised colour palette with set of 21 maximally contrasting colours
graph1D | Plot 1D graph of axis from multivariate analysis
heatplot | Draws heatmap with dendrograms.
html3D | Produce web page with a 3D graph that can be viewed using Chime web browser plug-in, and/or a pdb file that can be viewed using Rasmol
isDataFrame | Converts microarray input data into a data frame suitable for analysis in ADE4.
khan | Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
NCI60 | Microarray gene expression profiles of the NCI 60 cell lines
ord | Ordination
overview | Draw boxplot, histogram and hierarchical tree of gene expression data
plot.bga | Between group analysis
plot.cia | Coinertia analysis: Explore the covariance between two datasets
plot.ord | Ordination
plot.suppl | Projection of supplementary data onto axes from a between group analysis
plotarrays | Graph xy plot of variable (array) projections from ordination, between group analysis or coinertia analysis.
plotgenes | Graph xy plot of variable (gene) projections from PCA or COA. Only label variables at ends of axes
prettyDend | Draw hierarchical tree of gene expression data with a colorbar for numerous class vectors
print.comparelists | Return the intersect, difference and union between 2 vectors
randomiser | Randomly reassign training and test samples
rotate3d | Generate 3D graph(s) using scatterplot3d
sumstats | Summary statistics on xy co-ordinates, returns the slopes and distance from origin of each co-ordinate.
suppl | Projection of supplementary data onto axes from a between group analysis
topgenes | Topgenes, returns a list of variables at the ends (positive, negative or both) of an axis