Package: affycomp 1.89.0

Robert D. Shear

affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

Authors:Rafael A. Irizarry <[email protected]> and Zhijin Wu <[email protected]> with contributions from Simon Cawley <[email protected]>

affycomp_1.89.0.tar.gz
affycomp_1.89.0.zip(r-4.7)affycomp_1.89.0.zip(r-4.6)affycomp_1.89.0.zip(r-4.5)
affycomp_1.89.0.tgz(r-4.6-any)affycomp_1.89.0.tgz(r-4.5-any)
affycomp_1.89.0.tar.gz(r-4.7-any)affycomp_1.89.0.tar.gz(r-4.6-any)
affycomp_1.89.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
affycomp/json (API)

# Install 'affycomp' in R:
install.packages('affycomp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rafalab/affycomp/issues

Datasets:

On BioConductor:affycomp-1.89.0(bioc 3.24)affycomp-1.88.0(bioc 3.23)

onechannelmicroarraypreprocessing

6.14 score 23 scripts 712 downloads 13 mentions 64 exports 3 dependencies

Last updated from:958e3fe349. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR136
linux-devel-x86_64NOTE142
source / vignettesOK146
linux-release-x86_64NOTE126
macos-release-arm64NOTE112
macos-oldrel-arm64NOTE86
windows-develNOTE87
windows-releaseNOTE85
windows-oldrelNOTE137
wasm-releaseOK104

Exports:affycompaffycomp.compfig2affycomp.compfig2baffycomp.compfig3affycomp.compfig4aaffycomp.compfig4baffycomp.compfig4caffycomp.compfig5aaffycomp.compfig5baffycomp.compfig5caffycomp.compfig5cdeaffycomp.compfig5daffycomp.compfig5eaffycomp.compfig7affycomp.compfigsaffycomp.compfigs.callsaffycomp.figure.callsaffycomp.figure1affycomp.figure1baffycomp.figure2affycomp.figure2baffycomp.figure3affycomp.figure4aaffycomp.figure4baffycomp.figure4caffycomp.figure5aaffycomp.figure5baffycomp.figure5caffycomp.figure5daffycomp.figure5eaffycomp.figure6aaffycomp.figure6baffycomp.figure7affycomp.figuresaffycompPlotaffycompTableassessAllassessDilutionassessFCassessFC2assessLSassessMAassessMA2assessSDassessSignalassessSpikeInassessSpikeIn2assessSpikeInSDexprset.logread.dilutionread.newspikeinread.spikeinremove.hgu133a.xhybtableAlltableDilutiontableFCtableFC2tableLStableMA2tableOverallSNRtableRankstableSDtableSignaltableSpikeInSD

Dependencies:BiobaseBiocGenericsgenerics

affycomp primer

Rendered fromaffycomp.Rnwusingutils::Sweaveon May 29 2026.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Auxiliary functions to create comparitive Figuresaffycomp.compfig2 affycomp.compfig2b affycomp.compfig3 affycomp.compfig4a affycomp.compfig4b affycomp.compfig4c affycomp.compfig5a affycomp.compfig5b affycomp.compfig5c affycomp.compfig5cde affycomp.compfig5d affycomp.compfig5e affycomp.compfigs.auxiliary
Auxiliary functions to create Figuresaffycomp.figure1 affycomp.figure1b affycomp.figure2 affycomp.figure2b affycomp.figure3 affycomp.figure4a affycomp.figure4b affycomp.figure4c affycomp.figure5a affycomp.figure5b affycomp.figure5c affycomp.figure5d affycomp.figure5e affycomp.figure6a affycomp.figure6b affycomp.figures.auxiliary
Assessment Plotsaffycomp.compfigs affycomp.compfigs.calls affycomp.figure.calls affycomp.figures affycompPlot
Expression Assessment TableaffycompTable tableAll tableDilution tableFC tableFC2 tableLS tableMA2 tableOverallSNR tableRanks tableSignal tableSpikeInSD
Assessment functionsaffycomp assessAll
Assessment functions for Dilution DataassessDilution
SD Assessment functionsassessSD
Assessment functions for Spike In DataassessFC assessFC2 assessMA assessSignal assessSpikeIn
New Assessment functions for Spike In DataassessLS assessMA2 assessSpikeIn2 assessSpikeInSD
Phenotypic Information for Dilution Studydilution.phenodata
Take log base 2 of Expressionexprset.log
phenotypic information for HGU133A spike in studyhgu133a.spikein.phenodata
Cross hybridizershgu133a.spikein.xhyb
Example of the result of assessmentsmas5.assessment
Read Expression Date Setsread.dilution read.newspikein read.spikein readin
Remove crosshybridizersremove.hgu133a.xhyb
SD Assessment Functionsaffycomp.compfig7 affycomp.figure7 SD tableSD
phenotypic information for spike in studyspikein.phenodata