applera {applera}R Documentation

Class "applera" ~~~

Description

This is class representation for Applera Microarray Data.

Objects from the Class

Objects can be created by calls of the form new("applera", Organism= ..., #Object of class character, Geneid= ..., #Object of class vector, Signal= ..., #Object of class exprSet, Sdev= ..., #Object of class exprSet, Cv= ..., #Object of class exprSet, Sn= ..., #Object of class exprSet, Flags= ..., #Object of class exprSet, Ctrl= ..., #Object of class list.).

Slots

Organism:
Object of class "character" A string describing the organism implemented in the array: "Hs" for human, "Mm" for mouse, "Rn" for rat.
Geneid:
Object of class "character" A vector of primary Ids associated to spotted probes.
Signal:
Object of class "exprSet" it contains all the log2 chemiolominescence (CL) expression signals. The CL signal is normalized by the fluorescence (FL) signal over the feature integration aperture. See AB1700 manual.
Sdev:
Object of class "exprSet" An estimated measurement uncertainty of Normalized Signal. See ABI1700 manual.
Cv:
Object of class "exprSet" The fraction of uncertainty in the signal. Cv indicates the predicted spread of feature signal. See AB1700 manual.
Sn:
Object of class "exprSet" The ratio Signal/Sdev. S/N expresses the confidence of feature dectability. See AB1700 manual.
Flags:
Object of class "exprSet" A numeric code that identifies conditions for each feature. It allows to eliminate possibily problematic data. Features with flags greater than 100 might have quality issues. See AB1700 manual.
Ctrl:
Object of class "list" All controls spots values for Signal, Sdev, Cv, Sn and Flags. See ABI1700 manual.
exprs:
Object of class "exprMatrix" All data in slots Signal, Sdev, Cv, Sn and Flags are represented as exprSet object
se.exprs:
Object of class "exprMatrix" Not used
phenoData:
Object of class "phenoData" All data in slots Signal, Sdev, Cv, Sn and Flags contain the phenoData used to build the applera object
description:
Object of class "characterORMIAME" Not used
annotation:
Object of class "character" Not used
notes:
Object of class "character" Not used

Extends

Class "exprSet", directly.

Methods

apFilter
signature(apObj = "applera"): Function to filter an appleraSet by Sn or Flags
boxplot
signature(x = "applera"): Boxplot representation of slots data
ctrl
signature(object = "applera"): Function returning the list associated to the Ctrl slot
cvAp
signature(object = "applera"): Function returning the exprSet associated to the Cv slot
flags
signature(object = "applera"): Function returning the exprSet associated to the Flags slot
geneid
signature(object = "applera"): Function returning the Geneid slot
hist
signature(x = "applera"): Density distributions of slots data
iqrFilter
signature(apObj = "applera"): Function to filter an appleraSet, given a specific IQR values.
mvaAp
signature(apObj = "applera"): mva.pairs representation of Signal slot data
normLoess
signature(apObj = "applera"): Function to normalize an appleraSet using the normalize.loess function of the affy package
normQuantile
signature(apObj = "applera"): Function to normalize an appleraSet using the normalize.quantile function of the affy package
organism
signature(object = "applera"): Function returning the Organism slot
sdev
signature(object = "applera"): Function returning the exprSet associated to the Sdev slot
show
signature(object = "applera"): Renders information about the appleraSet in a concise way on stdout
signal
signature(object = "applera"): Function returning the exprSet associated to the Signal slot
sn
signature(object = "applera"): Function returning the exprSet associated to the Sn slot
subExp
signature(apObj = "applera"): Function to subset an appleraSet given a vector of sampleNames
subGenes
signature(apObj = "applera"): Function to subset an appleraSet given a vector of geneNames

Note

Author(s)

Raffaele A. Calogero <raffaele.calogero@unito.it>; Francesca Cordero <fcordero@di.unito.it>

References

See Also

readAp

Examples



[Package applera version 1.4.0 Index]