ExpressionSetIllumina-class {beadarray} | R Documentation

## Class "ExpressionSetIllumina"

### Description

Container for high-throughput assays and experimental metadata. `ExpressionSetIllumina` class is derived from `eSet`, and requires matrices `exprs`, `se.exprs`, `nObservations`, `Detection` as assay data members. The slots `featureData`, `phenoData` are accessed in the usual manner using `fData` and `pData` functions.

For `ExpressionSetIllumina` objects created from bead-level data (using the `summarize` function), a `QC` slot is used to contain any quality control data that was present in the `beadLevelData` object. This is a change from previous versions of beadarray, where the intensities of the control probes themselves were stored in this slot. From version 2.0.0 onwards, control probes are stored in the `assayData` slot with the regular probes and the `featureData` slot has a reference for which rows correspond to controls.

The `ExpressionSetIllumina` class is able to accomodate different channels when created from bead-level data. The `channelNames` function may be used to find out what channels are present in the object. The `channel` function can be used to select a particular channel, returning an `ExpressionSetIllumina` object.

### Author(s)

Mark Dunning

[Package beadarray version 2.40.0 Index]