maanova: Tools for analyzing Micro Array experiments

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

Author
Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui.
Date of publication
None
Maintainer
Keith Sheppard <keith.sheppard@jax.org>
License
GPL (>= 2)
Version
1.44.0
URLs

View on Bioconductor

Man pages

abf1
Data for a 18-array Affymetrix experiment
adjPval
Generate FDR adjusted P values for F test result.
arrayview
View the layout of input data
consensus
Build consensus tree out of bootstrap cluster result
dyeswapfilter
Gene filter for dye-swap experiment
fill.missing
Fill in missing data
fitmaanova
Fit ANOVA model for Micro Array experiment
fom
Figure of Merit
geneprofile
Expression plot for selected genes
gridcheck
Plot grid-by-grid data comparison for arrays
kidney
Kidney Data from CAMDA
maanova-internal
Internal maanova functions
macluster
Clustering analysis for Microarray experiment
matest
Statistical test for Microarray experiment
PairContrast
Pairwise comparison matrix
read.madata
Read Microarray data
resiplot
Residual plot for Microarray Experiment
riplot
Ratio intensity plot for 2-dye Microarray experiment
Rmaanova.version
Display the current version of the package
subset.madata
Subsetting Microarray data objects
summarytable
Summarize the matest result.
transform.madata
Micro Array experiment data transformation
varplot
Variance component plot
volcano
Volcano plot for F test results
write.madata
Write Micro Array data to a TAB delimited simple text file

Files in this package

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