prepdata

prepaffy

An object of class
  <code><a href="/link/ExpressionSet?package=arrayQuality&version=1.50.0&to=Biobase%3Aclass.ExpressionSet" rd-options="Biobase:class.ExpressionSet" data-mini-rdoc="Biobase:class.ExpressionSet::ExpressionSet">ExpressionSet</a></code> for one colour
  non Affymetrix data,
  <code><a href="/link/AffyBatch?package=arrayQuality&version=1.50.0&to=affy%3AAffyBatch-class" rd-options="affy:AffyBatch-class" data-mini-rdoc="affy:AffyBatch-class::AffyBatch">AffyBatch</a></code> for Affymetrix data,
  <code><a href="/link/NChannelSet?package=arrayQuality&version=1.50.0&to=Biobase%3Aclass.NChannelSet" rd-options="Biobase:class.NChannelSet" data-mini-rdoc="Biobase:class.NChannelSet::NChannelSet">NChannelSet</a></code> for two colour arrays, or
  <code><a href="/link/BeadLevelList?package=arrayQuality&version=1.50.0&to=beadarray%3Aclass-BeadLevelList" rd-options="beadarray:class-BeadLevelList" data-mini-rdoc="beadarray:class-BeadLevelList::BeadLevelList">BeadLevelList</a></code> for Illumina
  bead arrays.

expressionset

as in
    <code><a href="/link/arrayQualityMetrics?package=arrayQuality&version=1.50.0" rd-options="" data-mini-rdoc="arrayQuality::arrayQualityMetrics">arrayQualityMetrics</a></code>.

intgroup, do.logtransform

A list, typically the result from a prior call to <code>prepdata</code>.

<code>prepdata</code> computes summary statistics that are useful
  for all platforms; <code>prepaffy</code> computes Affymetrix-specific ones. These are
  helper functions used by <code><a href="/link/arrayQualityMetrics?package=arrayQuality&version=1.50.0" rd-options="" data-mini-rdoc="arrayQuality::arrayQualityMetrics">arrayQualityMetrics</a></code>.

Functions for performing print-run and array level
quality assessment.

Agnes Paquet

arrayQuality

Assessing array quality on spotted arrays

prepdata function

An object of class
  <code><a href="ExpressionSet" rd-options="Biobase:class.ExpressionSet">ExpressionSet</a></code> for one colour
  non Affymetrix data,
  <code><a href="AffyBatch" rd-options="affy:AffyBatch-class">AffyBatch</a></code> for Affymetrix data,
  <code><a href="NChannelSet" rd-options="Biobase:class.NChannelSet">NChannelSet</a></code> for two colour arrays, or
  <code><a href="BeadLevelList" rd-options="beadarray:class-BeadLevelList">BeadLevelList</a></code> for Illumina
  bead arrays.

as in
    <code><a href="arrayQualityMetrics" rd-options="">arrayQualityMetrics</a></code>.

<code>prepdata</code> computes summary statistics that are useful
  for all platforms; <code>prepaffy</code> computes Affymetrix-specific ones. These are
  helper functions used by <code><a href="arrayQualityMetrics" rd-options="">arrayQualityMetrics</a></code>.

prepdata: Compute useful summary statistics from a data object.

Description

Usage

Arguments

Value

Details