averageQuantile.AffymetrixCelSet

AffymetrixCelSet.averageQuantile

averageQuantile,AffymetrixCelSet-method

Calculates the average empirical distribution across all samples.

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.

Henrik Bengtsson

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

James Bullard

Kasper Hansen

Pierre Neuvial

Elizabeth Purdom

Mark Robinson

Ken Simpson

averageQuantile.AffymetrixCelSet function

<dl> <dt>probes</dt>
<dd>An optional <code><a href="/link/numeric?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code> specifying what subset of
 probes to be used to calculate the empirical distribution.
 If <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, all probes are used.</dd> <dt>...</dt>
<dd>Not used.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

If <code><a href="/link/NA?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NA">NA</a></code>s are detected in a sample, these are excluded and the
 <code><a href="/link/approx()?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::approx()">approx()</a></code> function (<code><a href="/link/approx?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::approx">approx</a></code>) is used to "expand"
 the <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code> of the remaining values so that the sorted <code><a href="/link/vector?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::vector">vector</a></code>
 (still) have length N.

Missing values

Author

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

<dl>

 <dt>probes</dt>
<dd>An optional <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> specifying what subset of
 probes to be used to calculate the empirical distribution.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, all probes are used.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

 <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd>

</dl>

If <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code>s are detected in a sample, these are excluded and the
 <code><a href='https://rdrr.io/r/stats/approxfun.html'>approx()</a></code> function (<code><a href='https://rdrr.io/r/stats/approxfun.html'>approx</a></code>) is used to "expand"
 the <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of the remaining values so that the sorted <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code>
 (still) have length N.

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

Description

Usage

Value

Arguments

Missing values

Author

Details

References

See Also