maanova: Tools for analyzing Micro Array experiments

Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("maanova")
AuthorHao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui.
Bioconductor views Clustering DifferentialExpression Microarray
Date of publicationNone
MaintainerKeith Sheppard <keith.sheppard@jax.org>
LicenseGPL (>= 2)
Version1.46.0
http://research.jax.org/faculty/churchill

View on Bioconductor

Functions

abf1 Man page
adjPval Man page
arrayview Man page
blkdiag Man page
buildtree Man page
caldf Man page
calPval Man page
calVolcanoXval Man page
check.confounding Man page
checkContrast Man page
cluster2num Man page
colmax Man page
colmin Man page
consensus Man page
consensus.hc Man page
consensus.kmean Man page
dist.cor Man page
dyeswapfilter Man page
fdr Man page
fill.missing Man page
findgroup Man page
fitmaanova Man page
fom Man page
geneprofile Man page
getPval.table Man page
getPval.volcano Man page
glowess Man page
gridcheck Man page
intprod Man page
JS Man page
JSshrinker Man page
kidney Man page
kidney.raw Man page
linlog Man page
linlog.engine Man page
linlogshift Man page
locateTerm Man page
macluster Man page
makeAB Man page
makeCompMat Man page
makeContrast Man page
makeD Man page
makeDesign Man page
makeHq Man page
makelevel Man page
makeModel Man page
make.ratio Man page
makeShuffleGroup Man page
makeZiZi Man page
matest Man page
matest.engine Man page
matest.perm Man page
matrank Man page
matsort Man page
meanvarlog Man page
meanvarlogold Man page
mixed Man page
mixture Man page
norm Man page
num2yn Man page
ones Man page
PairContrast Man page
parseformula Man page
pinv Man page
plot.consensus.hc Man page
plot.consensus.kmean Man page
print.madata Man page
print.summary.madata Man page
print.summary.mamodel Man page
ratioVarplot Man page
read.madata Man page
repmat Man page
resiplot Man page
riplot Man page
rlowess Man page
Rmaanova.version Man page
rowmax Man page
rowmin Man page
shift Man page
shuffle.maanova Man page
solveMME Man page
subset.madata Man page
summary.madata Man page
summary.mamodel Man page
summarytable Man page
summarytable.ftest Man page
summarytable.ttest Man page
sumrow Man page
transform.madata Man page
transform.rawdata Man page
varplot Man page
volcano Man page
volcano.ftest Man page
volcano.ttest Man page
write.madata Man page
zeros Man page

Files

DESCRIPTION
NAMESPACE
R
R/Rmaanova.version.R R/adjPval.R R/arrayview.R R/consensus.R R/dyeswapfileter.R R/fill.missing.R R/fitmaanova.R R/fom.R R/geneprofile.R R/gridcheck.R R/macluster.R R/makeModel.R R/matest.R R/matestutil.R R/mixed.R R/read.madata.R R/resiplot.R R/riplot.R R/subset.madata.R R/summarytable.R R/transform.madata.R R/util.R R/varplot.R R/volcano.R R/write.madata.R
build
build/vignette.rds
data
data/abf1.RData
data/kidney.RData
demo
demo/00Index
demo/abf1.R demo/kidney.R
inst
inst/LICENSE.txt
inst/README.txt
inst/STATUS.txt
inst/TODO.txt
inst/doc
inst/doc/maanova.Rnw
inst/doc/maanova.pdf
man
man/PairContrast.Rd man/Rmaanova.version.Rd man/abf1.Rd man/adjPval.Rd man/arrayview.Rd man/consensus.Rd man/dyeswapfilter.Rd man/fill.missing.Rd man/fitmaanova.Rd man/fom.Rd man/geneprofile.Rd man/gridcheck.Rd man/kidney.Rd man/maanova-internal.Rd man/macluster.Rd man/matest.Rd man/read.madata.Rd man/resiplot.Rd man/riplot.Rd man/subset.madata.Rd man/summarytable.Rd man/transform.madata.Rd man/varplot.Rd man/volcano.Rd man/write.madata.Rd
src
src/Makevars
src/Makevars.win
src/makeratio.c
src/masvd.c
src/masvd.h
src/shift.c
src/util.c
src/util.h
vignettes
vignettes/MPI.tex
vignettes/Rtour.tex
vignettes/abf1.tex
vignettes/abf1fig.pdf
vignettes/algorithm.tex
vignettes/arrayview.png
vignettes/camda.tex
vignettes/faq.tex
vignettes/gridcheck.png
vignettes/hckidney.pdf
vignettes/intro.tex
vignettes/maanova.Rnw
vignettes/maanova.bib
vignettes/paigen.tex
vignettes/prepfile.tex
vignettes/riplot.png
vignettes/rlowess.png
vignettes/vgprofile.pdf
vignettes/volcano.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.