calculateBaseline.ChipEffectSet

ChipEffectSet.calculateBaseline

calculateBaseline,ChipEffectSet-method

An <code><a href="/link/integer?package=aroma.affymetrix&version=1.6.0&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=1.6.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> specifying for which chromsosomes
    the baseline should be estimated.
    If <code><a href="/link/NULL?package=aroma.affymetrix&version=1.6.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>

chromosomes

An <code><a href="/link/integer?package=aroma.affymetrix&version=1.6.0&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> specifying the ploidy that the baseline
    should have.

ploidy

An <code><a href="/link/integer?package=aroma.affymetrix&version=1.6.0&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> specifying the default ploidy of
    chromosomes that have not explicitly been allocated one.

defaultPloidy

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=1.6.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, signals are averaged also for cells that are not
    on the genome.

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=1.6.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the CEL file that stores the is recreated.

force

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=1.6.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Estimates the baseline signal chromosome by chromosome.

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.

calculateBaseline.ChipEffectSet: Estimates the baseline signal chromosome by chromosome

Description

Usage

Arguments

See Also