A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]
DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities.  Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets).  In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit.  This speeds up the read substantially.  This package is supporting the Aroma framework and should not be used elsewhere.)

Copy-number analysis of large microarray data sets
Package for analysis of copy-number estimates obtained
from various platforms.
ProprietaryPlatforms, aCGH, CopyNumberVariants, SNP,
Microarray, OneChannel, TwoChannel, DataImport,
DataRepresentation, Preprocessing, QualityControl

Package for analysis of copy-number estimates obtained from various platforms.

Analysis of copy-number estimates obtained from various
platforms.

c( person("Henrik", "Bengtsson", role=c("aut", "cre",
"cph"), email="henrikb@braju.com"), person("Pierre", "Neuvial",
role="aut"))

c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Pierre", "Neuvial", role="aut"))
Methods for analyzing DNA copy-number data.  Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies.  It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.

Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]

Copy-Number Analysis of Large Microarray Data Sets

BioC (>= 3.0), Recommended: aroma.light, DNAcopy

Support package for aroma.affymetrix et al.
affxparser (>= 1.10.1), geneplotter (>= 1.16.0), RColorBrewer
(>= 1.0-2)
This package is a private support package for
aroma.affymetrix et al.  The methods and classes of this
package are independent of platform.  It's API is in alpha and
beta stage.