made4: Multivariate analysis of microarray data using ADE4

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Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.

Author
Aedin Culhane
Date of publication
None
Maintainer
Aedin Culhane <Aedin@jimmy.harvard.edu>
License
Artistic-2.0
Version
1.48.0
URLs

View on Bioconductor

Man pages

array2ade4
Converts microarray input data into a data frame suitable for...
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
checkfac
Check factor
chime3D
Produce web graph of 3D graph that can be viewed using Chime...
cia
Coinertia analysis: Explore the covariance between two...
commonMap
Highlight common points between two 1D plots
comparelists
Return the intersect, difference and union between 2 vectors
do3d
Generate 3D graph(s) using scatterplot3d
dudi.rwcoa
Row weighted Correspondence Analysis
forrwcoa
Row weighted Correspondence Analysis
genes
Returns an index of the top N variables at the ends of the x...
genes1d
genes1d: list top N variables on one axis. Lists the maximum...
getcol
Specialised colour palette with set of 21 maximally...
getdata
Check dataset
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...
jmol3D
Produce web graph of 3D graph that can be viewed using Jmol...
khan
Microarray gene expression dataset from Khan et al., 2001....
NCI60
Microarray gene expression profiles of the NCI 60 cell lines
ord
Ordination
overview
Draw boxplot, histogram and hierarchical tree of gene...
plotarrays
Graph xy plot of variable (array) projections from...
plotgenes
Graph xy plot of variable (gene) projections from PCA or COA....
prettyDend
Draw hierarchical tree of gene expression data with a...
randomiser
Randomly reassign training and test samples
sumstats
Summary statistics on xy co-ordinates, returns the slopes and...
suppl
Projection of supplementary data onto axes from a between...
s.var
Draw xy plots of results of multivariate analysis
topgenes
Topgenes, returns a list of variables at the ends (positive,...

Files in this package

made4/DESCRIPTION
made4/NAMESPACE
made4/R
made4/R/array2ade4.R
made4/R/bet.coinertia.R
made4/R/bga.R
made4/R/bga.jackknife.R
made4/R/bga.suppl.R
made4/R/checkfac.R
made4/R/cia.R
made4/R/commonMap.R
made4/R/comparelists.R
made4/R/do3d.R
made4/R/dudi.rwcoa.R
made4/R/forrwcoa.R
made4/R/getcol.R
made4/R/getdata.R
made4/R/graph1D.R
made4/R/heatplot.R
made4/R/html3D.R
made4/R/ord.R
made4/R/overview.R
made4/R/plotarrays.R
made4/R/plotgenes.R
made4/R/prettyDend.R
made4/R/randomiser.R
made4/R/rotate3d.R
made4/R/s.groups.R
made4/R/s.match.col.R
made4/R/s.var.R
made4/R/sumstats.R
made4/R/suppl.R
made4/R/topgenes.R
made4/build
made4/build/vignette.rds
made4/data
made4/data/NCI60.rda
made4/data/khan.rda
made4/inst
made4/inst/CITATION
made4/inst/doc
made4/inst/doc/introduction.R
made4/inst/doc/introduction.pdf
made4/inst/doc/introduction.rnw
made4/man
made4/man/NCI60.Rd
made4/man/array2ade4.Rd
made4/man/bet.coinertia.Rd
made4/man/between.graph.Rd
made4/man/bga.Rd
made4/man/bga.jackknife.Rd
made4/man/bga.suppl.Rd
made4/man/checkfac.Rd
made4/man/chime3D.Rd
made4/man/cia.Rd
made4/man/commonMap.Rd
made4/man/comparelists.Rd
made4/man/do3d.Rd
made4/man/dudi.rwcoa.Rd
made4/man/forrwcoa.Rd
made4/man/genes.Rd
made4/man/genes1d.Rd
made4/man/getcol.Rd
made4/man/getdata.Rd
made4/man/graph1D.Rd
made4/man/heatplot.Rd
made4/man/html3D.Rd
made4/man/jmol3D.Rd
made4/man/khan.Rd
made4/man/ord.Rd
made4/man/overview.Rd
made4/man/plotarrays.Rd
made4/man/plotgenes.Rd
made4/man/prettyDend.Rd
made4/man/randomiser.Rd
made4/man/s.var.Rd
made4/man/sumstats.Rd
made4/man/suppl.Rd
made4/man/topgenes.Rd
made4/vignettes
made4/vignettes/html3D.eps
made4/vignettes/html3D.pdf
made4/vignettes/introduction.rnw