extractExpressionSet.ChipEffectSet

ChipEffectSet.extractExpressionSet

extractExpressionSet,ChipEffectSet-method

extractExpressionSet

Optional argument passed to <code><a rd-options="aroma.affymetrix:extractMatrix.ChipEffectSet" href="/link/*extractMatrix?package=aroma.affymetrix&version=3.0.0&to=aroma.affymetrix%3AextractMatrix.ChipEffectSet" data-mini-rdoc="aroma.affymetrix:extractMatrix.ChipEffectSet::*extractMatrix">*extractMatrix</a>()</code>.

An <code><a rd-options="base" href="/link/integer?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::integer">integer</a></code> specifying the base to use when
   log-transforming the signals.  If <code><a rd-options="base" href="/link/NULL?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::NULL">NULL</a></code>, the signals are not
   transformed, but kept as is.

logBase

(optional) A <code><a rd-options="base" href="/link/character?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::character">character</a></code> string specifies a
   Bioconductor (ChipDb, CDF environment or PDInfo) annotation package,
   which then sets the 'annotation' slot of the returned object.
   If <code>"ChipDb"</code>, <code>"cdf"</code> or <code>"PDInfo"</code> th corresponding
   ChipDB, CDF environment or PDInfo package is inferred from
   the CDF's chip type.

annotationPkg

See <code><a rd-options="R.utils" href="/link/Verbose?package=aroma.affymetrix&version=3.0.0&to=R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose


 Extracts an in-memory ExpressionSet object from a <code><a rd-options="" href="/link/ChipEffectSet?package=aroma.affymetrix&version=3.0.0" data-mini-rdoc="aroma.affymetrix::ChipEffectSet">ChipEffectSet</a></code> object.
 Note that any modifications done to the extracted object will <em>not</em>
 be reflected in the original chip-effect set.


methods

internal

programming

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system.  The only parameter that limits the number of chips that can be processed is the amount of available disk space.  The Aroma Framework has successfully been used in studies to process tens of thousands of arrays.  This package has actively been used since 2006.

extractExpressionSet.ChipEffectSet: Extracts an in-memory ExpressionSet object

Description

Usage

Arguments

Value

See Also