normalizeQuantile.AffymetrixCelFile

AffymetrixCelFile.normalizeQuantile

normalizeQuantile,AffymetrixCelFile-method

The path where to save the normalized data files.

path

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 indices of 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 are updated.

subsetToUpdate

Types of probes to be updated.  For more details,
    see argument <code>types</code> of <code>identifyCells()</code> for the
    <code><a rd-options="" href="/link/AffymetrixCdfFile?package=aroma.affymetrix&version=3.0.0" data-mini-rdoc="aroma.affymetrix::AffymetrixCdfFile">AffymetrixCdfFile</a></code> class.

typesToUpdate

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

If <code><a rd-options="base:logical" href="/link/TRUE?package=aroma.affymetrix&version=3.0.0&to=base%3Alogical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, already normalized arrays are overwritten,
    unless skipped, otherwise an error is thrown.

overwrite

If <code><a rd-options="base:logical" href="/link/TRUE?package=aroma.affymetrix&version=3.0.0&to=base%3Alogical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the array is not normalized if it already exists.

skip

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 the probe intensities to a target 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.AffymetrixCelFile: Normalizes the probe intensities to a target empirical distribution

Description

Usage

Arguments

Value

See Also