AffyRNADegradation: Analyze and correct probe positional bias in microarray data due to RNA degradation
Version 1.22.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorMario Fasold
Bioconductor views GeneExpression Microarray OneChannel Preprocessing QualityControl
Date of publicationNone
MaintainerMario Fasold <fasold@izbi.uni-leipzig.de>
LicenseGPL-2
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AffyRNADegradation")

Man pages

AffyDegradationBatch-class: Class AffyDegradationBatch
AffyRNADegradation: Compute degradation parameters and correct probe intensities
AffyRNADegradation-package: AffyRNADegradation: analyze and correct RNA degradation...
GetTongs: Generate and visualize the tongs plot

Functions

AffyDegradationBatch Man page
AffyDegradationBatch,ANY Man page
AffyDegradationBatch-class Man page
AffyRNADegradation Man page
AffyRNADegradation-package Man page
ComputeTongs Source code
DecayFunction Source code
EstimateHookParams Source code
GetTongs Man page Source code
PlotDegradationHooks Man page Source code
PlotDx Source code
PlotTongs Man page Source code
ProbesetAverage Source code
ProbesetLogAverage Source code
RNADegradation Man page Source code
TryToFitDecayFunction Source code
afbatch Man page
afbatch,AffyDegradationBatch-method Man page
d Man page
d,AffyDegradationBatch-method Man page
getGeneralDegradationMeans Source code
getProbeInfo Source code
getProbeInfo.absolute Source code
getProbeInfo.index Source code
plotDx Man page
plotDx,AffyDegradationBatch-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AffyRNADegradation.R
R/AllClasses.R
R/decayFunction.R
R/probeInfo.R
R/tongs.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
man
man/AffyDegradationBatch-class.Rd
man/AffyRNADegradation-package.Rd
man/AffyRNADegradation.Rd
man/GetTongs.Rd
vignettes
vignettes/AffyRNADegradation.bib
vignettes/vignette.Rnw
AffyRNADegradation documentation built on May 20, 2017, 9:21 p.m.