plotDensity.AffymetrixCelSet

AffymetrixCelSet.plotDensity

plotDensity,AffymetrixCelSet-method

The subset of probes to considered <em>before</em> any
    filtering by probe type is applied.
    If a <code><a rd-options="base" href="/link/vector?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of <code><a rd-options="base" href="/link/double?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::double">double</a></code>s, the cell indices.
    If a scalar <code><a rd-options="base" href="/link/double?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::double">double</a></code> in [0,1], the fraction of cells, which can
    be used to speed up the plotting if approximate densities are
    acceptable.
    if <code><a rd-options="base" href="/link/NULL?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::NULL">NULL</a></code>, all cells are considered.
  

subset

The type of probes to include, e.g. <code>"all"</code>,
    <code>"pmmm"</code>, <code>"pm"</code>, and <code>"mm"</code>.

types

Additional arguments passed to
     <code><a rd-options="" href="/link/plotDensity.AffymetrixCelFile?package=aroma.affymetrix&version=3.0.0" data-mini-rdoc="aroma.affymetrix::plotDensity.AffymetrixCelFile">plotDensity.AffymetrixCelFile</a></code>().

A <code><a rd-options="base" href="/link/vector?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of colors for each of the arrays.

A <code><a rd-options="base" href="/link/vector?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of line types for each of the arrays.

A <code><a rd-options="base" href="/link/vector?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of line widths for each of the arrays.

If <code><a rd-options="base:logical" href="/link/FALSE?package=aroma.affymetrix&version=3.0.0&to=base%3Alogical" data-mini-rdoc="base:logical::FALSE">FALSE</a></code>, a new plot is created, otherwise the generated
    graphics is added to the current plot.

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.

plotDensity.AffymetrixCelSet: Plots the densities of all samples

Description

Usage

Arguments

Value

See Also