made4: Multivariate analysis of microarray data using ADE4

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

AuthorAedin Culhane
Date of publicationNone
MaintainerAedin Culhane <Aedin@jimmy.harvard.edu>
LicenseArtistic-2.0
Version1.48.0
http://www.hsph.harvard.edu/aedin-culhane/

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,...

Functions

array2ade4 Man page
bet.coinertia Man page
between.graph Man page
bga Man page
bga.jackknife Man page
bga.suppl Man page
checkfac Man page
chime3D Man page
cia Man page
commonMap Man page
comparelists Man page
do3d Man page
dudi.rwcoa Man page
forrwcoa Man page
genes Man page
genes1d Man page
getcol Man page
getdata Man page
graph1D Man page
heatplot Man page
html3D Man page
jmol3D Man page
khan Man page
NCI60 Man page
ord Man page
overview Man page
plotarrays Man page
plot.bga Man page
plot.cia Man page
plotgenes Man page
plot.ord Man page
plot.suppl Man page
prettyDend Man page
print.comparelists Man page
randomiser Man page
rotate3d Man page
s.groups Man page
s.match.col Man page
sumstats Man page
suppl Man page
s.var Man page
topgenes Man page

Files

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

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