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AffymetrixCelFile {aroma.affymetrix}

The AffymetrixCelFile class
Package: 
aroma.affymetrix
Version: 
2.11.1

Description

Package: aroma.affymetrix
Class AffymetrixCelFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile

Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class AffymetrixCelFile
extends AffymetrixFile

An AffymetrixCelFile object represents a single Affymetrix CEL file.

Usage

AffymetrixCelFile(..., cdf=NULL)

Arguments

...
Arguments passed to AromaMicroarrayDataFile.
cdf
An optional AffymetrixCdfFile making it possible to override the default CDF file as specified by the CEL file header. The requirement is that its number of cells must match that of the CEL file. If NULL, the CDF structure is inferred from the the chip type as specified in the CEL file header.

Fields and Methods

Methods:

extractMatrix -
getAm -
getCdf Gets the CDF structure for this CEL file.
getFileFormat -
getImage Creates an RGB Image object from a CEL file.
getUnitNamesFile -
getUnitTypesFile -
image270 Displays all or a subset of the data spatially.
nbrOfCells -
plotDensity Plots the density of the probe signals on the array.
plotImage Displays a spatial plot of a CEL file.
plotMvsA Plots log-ratio versus log-intensity in a scatter plot.
plotMvsX Plots log-ratio versus another variable in a scatter plot.
setCdf Sets the CDF structure for this CEL file.
smoothScatterMvsA Plots log-ratio versus log-intensity in a smooth scatter plot.
writeImage Writes a spatial image of the signals in the CEL file.

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, isGzipped, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

For developers

If you subclass this class, please make sure to query the AffymetrixCdfFile object (see *getCdf()) whenever querying CDF information. Do not use the CDF file inferred from the chip type in CEL header, unless you really want it to be hardwired that way, otherwise you will break to possibility to override the CDF structure.

See Also

An object of this class is typically part of an AffymetrixCelSet.

Author(s)

Henrik Bengtsson

Documentation reproduced from package aroma.affymetrix, version 2.11.1. License: LGPL (>= 2.1)