Package: made4 1.87.0

Aedin Culhane

made4: Multivariate analysis of microarray data using ADE4

Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.

Authors:Aedin Culhane

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
made4/json (API)

# Install 'made4' in R:

install.packages('made4', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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

On BioConductor:made4-1.87.0(bioc 3.24)made4-1.86.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

clustering classification dimensionreduction principalcomponent transcriptomics multiplecomparison geneexpression sequencing microarray

6.56 score 4 packages 150 scripts 746 downloads 86 mentions 32 exports 30 dependencies

Last updated from:f0dc10cacc. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	187
linux-devel-x86_64	NOTE	254
source / vignettes	OK	227
linux-release-x86_64	NOTE	260
macos-release-arm64	NOTE	203
macos-oldrel-arm64	NOTE	133
windows-devel	NOTE	193
windows-release	NOTE	200
windows-oldrel	NOTE	238
wasm-release	OK	106

Exports:asDataFrame bet.coinertia between.graph bga bga.jackknife bga.suppl cia commonMap comparelists do3d getcol graph1D heatplot html3D isDataFrame ord overview plot.bga plot.cia plot.ord plot.suppl plotarrays plotgenes prettyDend print.comparelists randomiser rotate3d s.groups s.var sumstats suppl topgenes

Dependencies:abind ade4 Biobase BiocGenerics bitops caTools DelayedArray generics GenomicRanges gplots gtools IRanges KernSmooth lattice MASS Matrix MatrixGenerics matrixStats pixmap RColorBrewer Rcpp RcppArmadillo S4Arrays S4Vectors scatterplot3d Seqinfo sp SparseArray SummarizedExperiment XVector

Introduction to Multivariate Analysis of Gene Expression Data using MADE4

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2020-10-14
Started: 2020-10-13

Citation

Development and contributors

Readme and manuals

Help Manual

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