computeAffinities.AffymetrixCdfFile

AffymetrixCdfFile.computeAffinities

computeAffinities,AffymetrixCdfFile-method

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> argument passed to <code>getProbeSequenceData()</code>.

safe

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>, cached results is returned, if available.

force

See <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>.

verbose

Calculates probe affinities from sequence.Adapted from <code><a rd-options="gcrma" href="/link/compute.affinities?package=aroma.affymetrix&version=3.0.0&to=gcrma" data-mini-rdoc="gcrma::compute.affinities">compute.affinities</a></code> in the gcrma package.
Attempts to find the tab-separated probe sequence file associated with
a particular CDF, and matches sequence to probe index in order to assign
an affinity to each probe.

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.

computeAffinities.AffymetrixCdfFile: Calculates probe affinities from sequence

Description

Usage

Arguments

Value