readRawData.AffymetrixCelFile

AffymetrixCelFile.readRawData

readRawData,AffymetrixCelFile-method

AffymetrixCelFile.getData

getData.AffymetrixCelFile

getData,AffymetrixCelFile-method

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> of cell indices.  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 cells
    are considered.

indices

fields

Additional arguments passed to <code><a href="/link/readCel?package=aroma.affymetrix&version=2.5.0&to=affxparser" rd-options="affxparser" data-mini-rdoc="affxparser::readCel">readCel</a></code>.

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> and a single field is returned, then data is
    returned as a <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>, otherwise as a <code><a href="/link/data.?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::data.">data.</a></code>

drop

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 <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

Gets all or a subset of the fields in a CEL file for all or a subset of the cells.

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").

readRawData.AffymetrixCelFile: Gets all or a subset of the fields in a CEL file

Description

Usage

Arguments

Value

Caching

See Also