plotDensity.AffymetrixCelFile

AffymetrixCelFile.plotDensity

plotDensity,AffymetrixCelFile-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="aroma.light" href="/link/plotDensity.numeric?package=aroma.affymetrix&version=3.0.0&to=aroma.light" data-mini-rdoc="aroma.light::plotDensity.numeric">plotDensity.numeric</a></code>.

xlim

xlab,ylab

If <code><a rd-options="base:logical" href="/link/TRUE?package=aroma.affymetrix&version=3.0.0&to=base%3Alogical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the density of the log (base 2) values are
     used, otherwise the non-logged values.

A <code><a rd-options="base" href="/link/logical?package=aroma.affymetrix&version=3.0.0&to=base" data-mini-rdoc="base::logical">logical</a></code> or a <code><a rd-options="R.utils" href="/link/Verbose?package=aroma.affymetrix&version=3.0.0&to=R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code> object.

verbose


 Plots the density of the probe signals on the array.


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.AffymetrixCelFile: Plots the density of the probe signals on the array

Description

Usage

Arguments

Value

See Also