bgAdjustOptical.AffymetrixCelSet

AffymetrixCelSet.bgAdjustOptical

bgAdjustOptical,AffymetrixCelSet-method

The location to save the adjusted data files.

path

The minimum adjusted intensity.  Defaults to 1.

minimum

The indices of 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 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 href="/link/AffymetrixCdfFile?package=aroma.affymetrix&version=2.5.0" rd-options="" data-mini-rdoc="aroma.affymetrix::AffymetrixCdfFile">AffymetrixCdfFile</a></code> class.

typesToUpdate

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=2.5.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, already adjusted arrays are overwritten,
    unless skipped, otherwise an error is thrown.

overwrite

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=2.5.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the array is not normalized if it already exists.

skip

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

.deprecated

Applies optical background correction to a set of CEL files.

 Adapted from <code><a href="/link/bg.adjust.optical?package=aroma.affymetrix&version=2.5.0&to=gcrma" rd-options="gcrma" data-mini-rdoc="gcrma::bg.adjust.optical">bg.adjust.optical</a></code> in the <pkg>gcrma</pkg> package.

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").

bgAdjustOptical.AffymetrixCelSet: Applies optical background correction to a set of CEL files

Description

Usage

Arguments

Value