BeadLevelList-class

arrayNames,BeadLevelList-method

getArrayData,BeadLevelList-method


A class for storing red and green channel foreground and background intensities from an Illumina experiment.


classes

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio.  Methods for quality assessment and low-level analysis are provided.

Mark Dunning

beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

BeadLevelList-class function

Objects can be created by calls of the form <code>new("BeadLevelList")</code>, but are usually created by <code><a rd-options="" href="/link/readIllumina?package=beadarray&version=2.22.2" data-mini-rdoc="beadarray::readIllumina">readIllumina</a></code>.

Objects from the Class

Objects of this class contain the following slots
  <table><tr><td>
  <code>beadData</code>:</td>
</tr><tr><td> an environment for storing the raw 
  bead-level data.  
  Each row correspond to a bead and columns the data.</td>
</tr><tr><td>
  <code>phenoData</code>:</td>
</tr><tr><td> an 'AnnotatedDataFrame' containing  
  experimental information.</td>
</tr><tr><td>
  <code>arrayInfo</code>:</td>
</tr><tr><td> a list containing array information.</td>
</tr><tr><td>
  <code>annotation</code>:</td>
</tr><tr><td> character storing annotation package 
    information.</td>
</tr></table>

Slots/List Components

<dl>
    <dt><code>arrayNames(object,arrays=NULL)</code></dt><dd>Returns the strip/array names from a
      <code>BeadLevelList</code> object for selected <code>arrays</code></dd> <dt><code>getArrayData(object,what="G",log=TRUE)</code></dt><dd>Retrieves 
      the <code>what</code> intensities on the <code>log</code> scale from the
      <code>BeadLevelList</code></dd> </dl> 

Methods

Objects can be created by calls of the form <code>new("BeadLevelList")</code>, but are usually created by <code><a rd-options='' href='readIllumina'>readIllumina</a></code>.

BeadLevelList-class: Class "BeadLevelList"

Description

Arguments

Objects from the Class

Slots/List Components

Methods