agilentDB

A dataset containing the Agilent probe Ids, and their GC content.These data allow <code><a href="/link/rCGH?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::rCGH">rCGH</a></code> to support Agilent aCGH arrays, from 44K to
400K. See the <code>source</code> section.This information is used to correct the GC% bias. For Agilent data only.

datasets

A comprehensive pipeline for analyzing and interactively 
    visualizing genomic profiles generated through commercial or custom aCGH
    arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction
    files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD
    probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or
    Affymetrix Power Tools. rCGH also supports custom arrays, provided data is
    in a suitable format. This package takes over all the steps required for
    individual genomic profiles analysis, from reading files to segmenting
    and annotating genes. This package provides several visualization functions
    (static or interactive) which facilitate individual profiles interpretation.
    Input files can be in compressed format, e.g. .bz2 or .gz.

Frederic Commo

rCGH

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

agilentDB function

A data frame with 411056 rows and 2 columns:
    <ul><li>ProbeID: Official Agilent probe ids.</li><li>GC: The GC content in each probe sequence, expressed as the
        GC fraction.</li></ul>

format

These data derive from the official Agilent Sequence List,
SurePrint_G3_Human_CGH_Microarray 2x400K_021850_D_SequenceList_20111015.txt,
freely available at: 
<href>https://earray.chem.agilent.com/suredesign/index.htm</href>{Agilent SureDesign}
Access date: 3-2-2015Notice that a User ID and Password are required to sign in.

source

A dataset containing the Agilent probe Ids, and their GC content.These data allow <code><a href="rCGH" rd-options="">rCGH</a></code> to support Agilent aCGH arrays, from 44K to
400K. See the <code>source</code> section.This information is used to correct the GC% bias. For Agilent data only.

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agilentDB: aCGH Agilent Probes GC Fraction

Description

Usage

Arguments

Value

format

source