Basic RNA Degradation Analysis | Using Absolute Probe Locations | Creating Custom Probe Location Files | Correction of the Bias and Integration into the Microarray Calibration Pipeline | Citing AffyRNADegradation | Details
Package: AffyRNADegradation 1.59.0
Mario Fasold
AffyRNADegradation: Analyze and correct probe positional bias in microarray data due to RNA degradation
The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
Authors:
AffyRNADegradation_1.59.0.tar.gz
AffyRNADegradation_1.59.0.zip(r-4.7)AffyRNADegradation_1.59.0.zip(r-4.6)AffyRNADegradation_1.59.0.zip(r-4.5)
AffyRNADegradation_1.59.0.tgz(r-4.6-any)AffyRNADegradation_1.59.0.tgz(r-4.5-any)
AffyRNADegradation_1.59.0.tar.gz(r-4.7-any)AffyRNADegradation_1.59.0.tar.gz(r-4.6-any)
AffyRNADegradation_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AffyRNADegradation/json (API)
| # Install 'AffyRNADegradation' in R: |
| install.packages('AffyRNADegradation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:AffyRNADegradation-1.59.0(bioc 3.24)AffyRNADegradation-1.58.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionmicroarrayonechannelpreprocessingqualitycontrol
Last updated from:1e3deb12ff. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 171 | ||
| linux-devel-x86_64 | NOTE | 243 | ||
| source / vignettes | OK | 251 | ||
| linux-release-x86_64 | NOTE | 232 | ||
| macos-release-arm64 | NOTE | 119 | ||
| macos-oldrel-arm64 | NOTE | 127 | ||
| windows-devel | NOTE | 563 | ||
| windows-release | NOTE | 514 | ||
| windows-oldrel | NOTE | 526 | ||
| wasm-release | OK | 137 |
Exports:afbatchdGetTongsPlotDegradationHooksplotDxPlotTongsRNADegradation
Dependencies:affyaffyioBiobaseBiocGenericsBiocManagergenericspreprocessCore
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class AffyDegradationBatch | afbatch afbatch,AffyDegradationBatch-method AffyDegradationBatch AffyDegradationBatch,ANY AffyDegradationBatch-class d d,AffyDegradationBatch-method plotDx plotDx,AffyDegradationBatch-method |
| AffyRNADegradation: analyze and correct RNA degradation effects | AffyRNADegradation-package AffyRNADegradation |
| Generate and visualize the tongs plot | GetTongs PlotDegradationHooks PlotTongs |
| Compute degradation parameters and correct probe intensities | RNADegradation |