Multivariate analysis of microarray data using ADE4

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Documentation for package ‘made4’ version 1.83.0

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