Package: affycomp 1.83.0
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_1.83.0.tar.gz
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affycomp_1.83.0.tgz(r-4.4-any)affycomp_1.83.0.tgz(r-4.3-any)
affycomp_1.83.0.tar.gz(r-4.5-noble)affycomp_1.83.0.tar.gz(r-4.4-noble)
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affycomp.pdf |affycomp.html✨
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
- 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-1.81.0(bioc 3.20)affycomp-1.80.0(bioc 3.19)
onechannelmicroarraypreprocessing
Last updated 23 days agofrom:0f0f8ff843. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | ERROR | Oct 30 2024 |
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:BiobaseBiocGenerics
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 |
