normalizeQuantile.AffymetrixCelSet

AffymetrixCelSet.normalizeQuantile

normalizeQuantile,AffymetrixCelSet-method

The path where to save the normalized data files.
    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>, 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 rd-options="base" href="/link/NULL?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::NULL">NULL</a></code>, all probes are updated.

subsetToUpdate

typesToUpdate

A <code><a rd-options="base" href="/link/numeric?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=aroma.affymetrix&version=3.0.0&to=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 rd-options="base" href="/link/numeric?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> in (0,1), then this
    fraction of all probes will be used.
    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>, all probes are considered.

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 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


 Normalizes samples to have the same empirical distribution.


methods

internal

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.

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

Description

Usage

Arguments

Value

See Also