class-ExpressionSetIllumina: Class "ExpressionSetIllumina"

In markdunning/beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

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

markdunning/beadarray documentation built on May 9, 2019, 8:35 a.m.