Class "beadData"

Description

A class to hold data information from a BeadChip experiment

Objects from the Class

Objects can be created by calls of the form new("beadData", ...).

Slots

fileOrigin:

Object of class "character": File paths of the data used to create the object

param:

Object of class "list": Parameters extracted from the source files

normMethod:

Object of class "character": The normalisation method applied to the object (if any)

detExprs:

Object of class "matrix": BeadStudio detection scores

exprs:

Object of class "exprMatrix": Unlogged intensity data

se.exprs:

Object of class "exprMatrix": Standard errors of bead replicates

description:

Object of class "character OR MIAME"

annotation:

Object of class "character": A name given to the analysis

notes:

Object of class "character": Notes

reporterInfo:

Object of class "data.frame Or NULL": reporter info

phenoData:

Object of class "phenoData": Phenotype data

Extends

Class "exprSet", directly. Class "annotatedDataset", by class "exprSet".

Methods

[

signature(x = "beadData"): subset for samples

boxplot

signature(x = "beadData"): boxplot of expression data

detectionCalls

signature(object = "beadData"): Obtain detection calls

detExprs

signature(object = "beadData"): slot accessor method

fileOrigin

signature(object = "beadData"): slot accessor method

nGenes

signature(object = "beadData"): Number of transcripts

normMethod

signature(object = "beadData"): slot accessor method

nSamples

signature(object = "beadData"): Number of samples

pairs

signature(x = "beadData"): Plot pairwise intensity plots

param

signature(object = "beadData"): slot accessor method

signalMeans

signature(object = "beadData"): Obtain signal means

summary

signature(object = "beadData"): Obtain summary of the data

Author(s)

Gareth Elvidge gareth.elvidge@well.ox.ac.uk

Examples

data(examplebeadData)
nGenes(examplebeadData)