| applera {applera} | R Documentation |
This is class representation for Applera Microarray Data.
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.).
Organism:"character" A string describing the organism implemented in the array: "Hs" for human, "Mm" for mouse, "Rn" for rat. Geneid:"character" A vector of primary Ids associated to spotted probes. Signal:"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:"exprSet" An estimated measurement uncertainty of Normalized Signal. See ABI1700 manual. Cv:"exprSet" The fraction of uncertainty in the signal. Cv indicates the predicted spread of feature signal. See AB1700 manual. Sn:"exprSet" The ratio Signal/Sdev. S/N expresses the confidence of feature dectability. See AB1700 manual. Flags:"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:"list" All controls spots values for Signal, Sdev, Cv, Sn and Flags. See ABI1700 manual. exprs:"exprMatrix" All data in slots Signal, Sdev, Cv, Sn and Flags are represented as exprSet object se.exprs:"exprMatrix" Not used phenoData:"phenoData" All data in slots Signal, Sdev, Cv, Sn and Flags contain the phenoData used to build the applera objectdescription:"characterORMIAME" Not used annotation:"character" Not used notes:"character" Not used
Class "exprSet", directly.
signature(apObj = "applera"): Function to filter an appleraSet by Sn or Flagssignature(x = "applera"): Boxplot representation of slots data signature(object = "applera"): Function returning the list associated to the Ctrl slot signature(object = "applera"): Function returning the exprSet associated to the Cv slot signature(object = "applera"): Function returning the exprSet associated to the Flags slot signature(object = "applera"): Function returning the Geneid slot signature(x = "applera"): Density distributions of slots data signature(apObj = "applera"): Function to filter an appleraSet, given a specific IQR values. signature(apObj = "applera"): mva.pairs representation of Signal slot data signature(apObj = "applera"): Function to normalize an appleraSet using the normalize.loess function of the affy package signature(apObj = "applera"): Function to normalize an appleraSet using the normalize.quantile function of the affy package signature(object = "applera"): Function returning the Organism slot signature(object = "applera"): Function returning the exprSet associated to the Sdev slot signature(object = "applera"): Renders information about the appleraSet in a concise way on stdout signature(object = "applera"): Function returning the exprSet associated to the Signal slot signature(object = "applera"): Function returning the exprSet associated to the Sn slot signature(apObj = "applera"): Function to subset an appleraSet given a vector of sampleNames signature(apObj = "applera"): Function to subset an appleraSet given a vector of geneNames Raffaele A. Calogero <raffaele.calogero@unito.it>; Francesca Cordero <fcordero@di.unito.it>