getAlleleProbePairs.AffymetrixCdfFile

AffymetrixCdfFile.getAlleleProbePairs

getAlleleProbePairs,AffymetrixCdfFile-method

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

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.

Henrik Bengtsson

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

James Bullard

Kasper Hansen

Pierre Neuvial

Elizabeth Purdom

Mark Robinson

Ken Simpson

getAlleleProbePairs.AffymetrixCdfFile function

<dl> <dt>verbose</dt>
<dd>A <code><a href="/link/logical?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::logical">logical</a></code> or a <code>Verbose</code> object.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:<dl>
 <dt>Mapping10K_Xba142</dt>
<dd>10208 units &amp; 432964 cells: 11 seconds.</dd> <dt>Mapping50K_Xba240</dt>
<dd>58960 SNPs &amp; 589,600 (PMA,PMB) probe pairs: 11 seconds.</dd> 
</dl>

Benchmarking

Author

Gets the indices of probepairs with the same pair of SNP nucleotides — getAlleleProbePairs.AffymetrixCdfFile

<dl>

 <dt>verbose</dt>
<dd>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> or a <code>Verbose</code> object.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

</dl>

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:<dl>
 <dt>Mapping10K_Xba142</dt>
<dd>10208 units &amp; 432964 cells: 11 seconds.</dd>

 <dt>Mapping50K_Xba240</dt>
<dd>58960 SNPs &amp; 589,600 (PMA,PMB) probe pairs: 11 seconds.</dd>

 
</dl>

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

Description

Usage

Value

Arguments

Benchmarking

Author

See Also