getImage.AffymetrixCelFile

AffymetrixCelFile.getImage

getImage,AffymetrixCelFile-method

An optional <code><a href="/link/AffymetrixCelFile?package=aroma.affymetrix&version=2.5.0" rd-options="" data-mini-rdoc="aroma.affymetrix::AffymetrixCelFile">AffymetrixCelFile</a></code> of the same chip type,
     that is used for calculating the ratio (non-logged).  Note, to get
     the log-ratios, the <code>log</code>() function has to be specif

other

<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>s of length two specifying the
     (x0,x1) and (y0,y1) regions to be extracted.  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>, the
     complete regions is used.

xrange, yrange

One of the CEL file fields, i.e. <code>"intensities"</code>,
     <code>stdvs</code>, or <code>pixels</code>.

field

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> scale factor in (0,+Inf) for resizing the
    imaging. If <code>1</code>, no resizing is done.

zoom

An optional <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> of color code.

palette

Additional arguments passed to
     <code><a href="/link/*readRawDataRectangle?package=aroma.affymetrix&version=2.5.0&to=aroma.affymetrix%3AreadRawDataRectangle.AffymetrixCelFile" rd-options="aroma.affymetrix:readRawDataRectangle.AffymetrixCelFile" data-mini-rdoc="aroma.affymetrix:readRawDataRectangle.AffymetrixCelFile::*readRawDataRectangle">*readRawDataRectangle</a>()</code> and more function.

A <code><a href="/link/function?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::function">function</a></code> taking arguments 'xrange' and 'yrange',
    or <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> for the default read function.

readRectFcn

A <code><a href="/link/logical?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::logical">logical</a></code> or a <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> object.

verbose

Creates an RGB Image object from a CEL file.

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").

getImage.AffymetrixCelFile: Creates an RGB Image object from a CEL file

Description

Usage

Arguments

Value

See Also