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 as`dim`, `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]