normalizeQuantile.AffymetrixCelSet

AffymetrixCelSet.normalizeQuantile

normalizeQuantile,AffymetrixCelSet-method

The path where to save the normalized data files.
    If <code><a href="/link/NULL?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, a default name is used.

path

The name of the normalized data set, which will also be
    part of the default path.

name

The probes to be updated.
    If <code><a href="/link/NULL?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, all probes are updated.

subsetToUpdate

typesToUpdate

A <code><a href="/link/numeric?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code>.  The empirical distribution
    to which all arrays should be normalized to.

xTarget

The probes to calculate average empirical
    distribution over.  If a single <code><a href="/link/numeric?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> in (0,1), then this
    fraction of all probes will be used.
    If <code><a href="/link/NULL%3C%2F?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::NULL</">NULL</</a></code>

subsetToAvg

Types of probes to be used when calculating the
    average empirical distribution.
    If <code>"pm"</code> and <code>"mm"</code> only perfect-match and mismatch
    probes are used, respectively. If <code>"pmmm"</code> both types are used.

typesToAvg

Additional arguments passed to <code>normalizeQuantile()</code>.

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.5.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Normalizes samples to have the same empirical distribution.

methods

internal

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 diskspace that limits the number of arrays that
        can be analyzed.  To install, do:
        source("http://www.aroma-project.org/hbLite.R");
        hbInstall("aroma.affymetrix").

normalizeQuantile.AffymetrixCelSet: Normalizes samples to have the same empirical distribution

Description

Usage

Arguments

Value

See Also