getAlleleProbePairs3.AffymetrixCdfFile

AffymetrixCdfFile.getAlleleProbePairs3

getAlleleProbePairs3,AffymetrixCdfFile-method

A <code><a href="/link/logical?package=aroma.affymetrix&version=2.5.0&to=base" rd-options="base" data-mini-rdoc="base::logical">logical</a></code> or a <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.5.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code> object.

verbose

Gets the indices of probepairs with the same pair of SNP nucleotides.
  Note that the order of allele A and allele B is irrelevant.
  For instance, all probepairs with nucleotides (A,T) are calibrated
  together with all probepairs with nucleotides (T,A) reversed.

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.  To install, do:
        source("http://www.aroma-project.org/hbLite.R");
        hbInstall("aroma.affymetrix").

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

getAlleleProbePairs3.AffymetrixCdfFile function

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:
  <ul><li>Mapping10K\_Xba142</li></ul>{10208 units & 432964 cells: 11 seconds.}
   <item>Mapping50K_Xba240</item>{58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.}

getAlleleProbePairs3.AffymetrixCdfFile: Gets the indices of probepairs with the same pair of SNP nucleotides

Description

Usage

Arguments

Value

Benchmarking

See Also