extractExpressionSet.ChipEffectSet

ChipEffectSet.extractExpressionSet

extractExpressionSet,ChipEffectSet-method

extractExpressionSet

Optional argument passed to <code><a href="/link/*extractMatrix?package=aroma.affymetrix&version=2.11.1&to=aroma.affymetrix%3AextractMatrix.ChipEffectSet" rd-options="aroma.affymetrix:extractMatrix.ChipEffectSet" data-mini-rdoc="aroma.affymetrix:extractMatrix.ChipEffectSet::*extractMatrix">*extractMatrix</a>()</code>.

An <code><a href="/link/integer?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> specifying the base to use when
   log-transforming the signals.  If <code><a href="/link/NULL?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, the signals are not
   transformed, but kept as is.

logBase

(optional) A <code><a href="/link/character?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="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>

annotationPkg

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.11.1&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Extracts an in-memory ExpressionSet object from a <code><a href="/link/ChipEffectSet?package=aroma.affymetrix&version=2.11.1" rd-options="" 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

This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.  These are designed to be memory efficient but still being fast.  The idea is to keep all data on file and only read data into memory when needed.  Clever caching mechanisms are used to minimize the overhead of data IO.  All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory.  With this design it is only the disk space that limits the number of arrays that can be analyzed.

extractExpressionSet.ChipEffectSet: Extracts an in-memory ExpressionSet object

Description

Usage

Arguments

Value

See Also