Introduction | What's new in version 1.2? | The Image Report | The end
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:
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✨
DESCRIPTION
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:
- dilution.phenodata - Phenotypic Information for Dilution Study
- hgu133a.spikein.phenodata - Phenotypic information for HGU133A spike in study
- hgu133a.spikein.xhyb - Cross hybridizers
- mas5.assessment - Example of the result of assessments
- spikein.phenodata - Phenotypic information for spike in study
On BioConductor:affycomp-1.89.0(bioc 3.24)affycomp-1.88.0(bioc 3.23)
onechannelmicroarraypreprocessing
Last updated from:958e3fe349. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 150 | ||
| linux-devel-x86_64 | NOTE | 200 | ||
| source / vignettes | OK | 194 | ||
| linux-release-x86_64 | NOTE | 137 | ||
| macos-release-arm64 | NOTE | 74 | ||
| macos-oldrel-arm64 | NOTE | 94 | ||
| windows-devel | NOTE | 102 | ||
| windows-release | NOTE | 81 | ||
| windows-oldrel | NOTE | 83 | ||
| wasm-release | OK | 94 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Auxiliary functions to create comparitive Figures | affycomp.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 Figures | affycomp.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 Plots | affycomp.compfigs affycomp.compfigs.calls affycomp.figure.calls affycomp.figures affycompPlot |
| Expression Assessment Table | affycompTable tableAll tableDilution tableFC tableFC2 tableLS tableMA2 tableOverallSNR tableRanks tableSignal tableSpikeInSD |
| Assessment functions | affycomp assessAll |
| Assessment functions for Dilution Data | assessDilution |
| SD Assessment functions | assessSD |
| Assessment functions for Spike In Data | assessFC assessFC2 assessMA assessSignal assessSpikeIn |
| New Assessment functions for Spike In Data | assessLS assessMA2 assessSpikeIn2 assessSpikeInSD |
| Phenotypic Information for Dilution Study | dilution.phenodata |
| Take log base 2 of Expression | exprset.log |
| phenotypic information for HGU133A spike in study | hgu133a.spikein.phenodata |
| Cross hybridizers | hgu133a.spikein.xhyb |
| Example of the result of assessments | mas5.assessment |
| Read Expression Date Sets | read.dilution read.newspikein read.spikein readin |
| Remove crosshybridizers | remove.hgu133a.xhyb |
| SD Assessment Functions | affycomp.compfig7 affycomp.figure7 SD tableSD |
| phenotypic information for spike in study | spikein.phenodata |
