AffyDegradationBatch-class {AffyRNADegradation} | R Documentation |
This class represents Affymetrix GeneChip probe level data that has been analysed and corrected for the probe location bias.
Objects can be created using the function RNADegradation
.
location.type
:Object of class character
describing the type of probe position used for the analysis (probe index or probe location).
afbatch
:Object of class AffyBatch
containing
corrected probe level data.
stats
:Object of class matrix
containg various
statistical parameters from the analysis.
means.pm
:Object of class matrix
containing the average PM probe intensites for probe locations of
expressed genes.
means.mm
:Object of class matrix
containing the average MM probe intensites for probe locations of
expressed genes.
signature(x = "AffyDegradationBatch")
: returns
as AffyBatch
object containing corrected probe level data.
signature(x = "AffyDegradationBatch")
: returns
a vector with a measure of RNA degradation for each sample
signature(x = "AffyDegradationBatch")
: plots the
probe location bias for all samples of the experiment.
Mario Fasold
AffyBatch
if (require(AmpAffyExample)) { # Get example data data(AmpData) affy.deg <- RNADegradation(AmpData[,4]) ## Plot degradation plotDx(affy.deg) ## Get degradation measure d(affy.deg) ## Get AffyBatch object with corrected probe intensities afbatch(affy.deg) }