BeadSummaryList-class {beadarray}R Documentation

Stores bead summary data - class

Description

A list based class for storing bead summary data. BeadSummaryList objects can be created from BeadLevelList objects or by reading directly from pre-processed BeadStudio output by using the readBeadSummaryData function.

Slots/List Components

Objects should contain the following list components:
R: Numeric matrix containing foreground intensites for the red channel. Rows correspond to beadtypes and columns to arrays.
Rb: Numeric matrix containing background intensites for the red channel.
BeadStDev: Standard deviations for each bead type per array.
NoBeads: Number of beads of each type per array.
ProbeID: ID for each probe on the arrays.
nooutliers: The number of beads flagged as outliers for each bead type per array. This is only used for bead summary data created by beadarray and not for pre-processed data read from BeadStudio

Methods

BeadSummaryLists can be subsetted and combined. They also return dimensions so functions such asdim, nrow and ncol are also defined. BeadSummaryList uses an adapted version of the show method from the Limma class LargeDataObject. This means that the BeadSummaryList will print in a relatively compact way.

Other functions which operate on BeadSummaryList objects include: plotXY.beads plotMA.beads getMeanIntensities pairwiseMA

Author(s)

Mark Dunning and Mike Smith


[Package beadarray version 1.0.0 Index]