averageQuantile.AffymetrixCelSet

AffymetrixCelSet.averageQuantile

averageQuantile,AffymetrixCelSet-method

An optional <code><a href="/link/numeric?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> specifying what subset of
      probes to be used to calculate the empirical distribution.
      If <code></code>

probes

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.2.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Calculates the average empirical distribution across all samples.

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").

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

averageQuantile.AffymetrixCelSet function

If <code><a href="/link/NA?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::NA">NA</a></code>s are detected in a sample, these are excluded and the
   <code>approx()</code> function (<code><a href="/link/approx?package=aroma.affymetrix&version=2.2.0&to=stats" rd-options="stats" data-mini-rdoc="stats::approx">approx</a></code>) is used to "expand"
   the <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of the remaining values so that the sorted <code><a href="/link/vector?package=aroma.affymetrix&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code>
   (still) have length N.

averageQuantile.AffymetrixCelSet: Calculates the average empirical distribution across all samples

Description

Usage

Arguments

Value

Missing values

Details

References

See Also