Package: aroma.affymetrix 3.2.2

aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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.

Authors:Henrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb]

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NEWS

# Install 'aroma.affymetrix' in R:

install.packages('aroma.affymetrix', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/henrikbengtsson/aroma.affymetrix/issues

On CRAN:

infrastructure proprietaryplatforms exonarray microarray onechannel gui dataimport datarepresentation preprocessing qualitycontrol visualization reportwriting acgh copynumbervariants differentialexpression geneexpression snp transcription affymetrix analysis copy-number dna expression hpc large-scale notebook reproducibility rna

5.70 score 10 stars 3 packages 112 scripts 792 downloads 1685 exports 24 dependencies

Last updated 9 months agofrom:4e3d784440 (on master). Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win	NOTE	Nov 14 2024
R-4.5-linux	NOTE	Nov 14 2024
R-4.4-win	OK	Nov 14 2024
R-4.4-mac	OK	Nov 14 2024
R-4.3-win	OK	Nov 14 2024
R-4.3-mac	OK	Nov 14 2024

Dependencies:aroma.apd aroma.core aroma.light base64enc BiocManager codetools digest DNAcopy future globals listenv MASS matrixStats parallelly PSCBS R.cache R.devices R.filesets R.huge R.methodsS3 R.oo R.rsp R.utils RColorBrewer

Help page	Topics
Package aroma.affymetrix	aroma.affymetrix-package aroma.affymetrix
The AbstractProbeSequenceNormalization class	AbstractProbeSequenceNormalization
The AdditiveCovariatesNormalization class	AdditiveCovariatesNormalization
The AffineCnPlm class	AffineCnPlm
The AffinePlm class	AffinePlm
The AffineSnpPlm class	AffineSnpPlm
The AffymetrixCdfFile class	AffymetrixCdfFile
The AffymetrixCelFile class	AffymetrixCelFile
The AffymetrixCelSet class	AffymetrixCelSet nbrOfArrays.AffymetrixCelSet
The AffymetrixCelSetReporter class	AffymetrixCelSetReporter
The AffymetrixCelSetTuple class	AffymetrixCelSetTuple
The AffymetrixCnChpSet class	AffymetrixCnChpSet
The abstract AffymetrixFile class	AffymetrixFile
The AffymetrixFileSet class	AffymetrixFileSet
The AffymetrixFileSetReporter class	AffymetrixFileSetReporter
The AffymetrixPgfFile class	AffymetrixPgfFile
The AlleleSummation class	AlleleSummation
The AllelicCrosstalkCalibration class	AllelicCrosstalkCalibration
The AromaChipTypeAnnotationFile class	AromaChipTypeAnnotationFile
The ArrayExplorer class	ArrayExplorer
The AvgCnPlm class	AvgCnPlm
The AvgPlm class	AvgPlm
The AvgSnpPlm class	AvgSnpPlm
The BackgroundCorrection class	BackgroundCorrection
The BaseCountNormalization class	BaseCountNormalization
The BasePositionNormalization class	BasePositionNormalization
The ChipEffectFile class	ChipEffectFile
The ChipEffectSet class	ChipEffectSet
The ChipEffectTransform class	ChipEffectTransform
The CnagCfhFile class	CnagCfhFile
The CnagCfhSet class	CnagCfhSet
The CnChipEffectFile class	CnChipEffectFile
The CnChipEffectSet class	CnChipEffectSet
The CnPlm class	CnPlm
The CnProbeAffinityFile class	CnProbeAffinityFile
The CrlmmParametersFile class	CrlmmParametersFile
The CrlmmParametersSet class	CrlmmParametersSet
The DChipCdfBinFile class	DChipCdfBinFile
The DChipDcpFile class	DChipDcpFile
The DChipDcpSet class	DChipDcpSet
The DChipGenomeInformation class	DChipGenomeInformation
The DChipQuantileNormalization class	DChipQuantileNormalization
The DChipSnpInformation class	DChipSnpInformation
Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)	doASCRMAv1 doASCRMAv1.default doCRMAv1 doCRMAv1.AffymetrixCelSet doCRMAv1.default
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)	doASCRMAv2 doASCRMAv2.default doCRMAv2 doCRMAv2.AffymetrixCelSet doCRMAv2.default
Finding Isoforms using Robust Multichip Analysis (FIRMA)	doFIRMA doFIRMA.AffymetrixCelSet doFIRMA.default
Robust Multichip Analysis (GCRMA)	doGCRMA doGCRMA.AffymetrixCelSet doGCRMA.default
Robust Multichip Analysis (RMA)	doRMA doRMA.AffymetrixCelSet doRMA.default
The ExonChipEffectFile class	ExonChipEffectFile
The ExonChipEffectSet class	ExonChipEffectSet
The ExonProbeAffinityFile class	ExonProbeAffinityFile
The ExonRmaPlm class	ExonRmaPlm
The FirmaFile class	FirmaFile
The FirmaModel class	FirmaModel
The FirmaSet class	FirmaSet
The FragmentEquivalentClassNormalization class	FragmentEquivalentClassNormalization
The FragmentLengthNormalization class	FragmentLengthNormalization
The GcContentNormalization class	GcContentNormalization
The GcContentNormalization2 class	GcContentNormalization2
The GcRmaBackgroundCorrection class	GcRmaBackgroundCorrection
The GenericReporter class	GenericReporter
The GenomeInformation class	GenomeInformation
The HetLogAddCnPlm class	HetLogAddCnPlm
The HetLogAddPlm class	HetLogAddPlm
The HetLogAddSnpPlm class	HetLogAddSnpPlm
Robust Multichip Analysis (RMA) reproducing the affy package	justRMA justRMA.AffymetrixCelSet justRMA.default
The LimmaBackgroundCorrection class	LimmaBackgroundCorrection
The LinearModelProbeSequenceNormalization class	LinearModelProbeSequenceNormalization
The MatNormalization class	MatNormalization
The MatSmoothing class	MatSmoothing
The MbeiCnPlm class	MbeiCnPlm
The MbeiPlm class	MbeiPlm
The MbeiSnpPlm class	MbeiSnpPlm
The Model class	Model
The MultiArrayUnitModel class	MultiArrayUnitModel
The NormExpBackgroundCorrection class	NormExpBackgroundCorrection
The OpticalBackgroundCorrection class	OpticalBackgroundCorrection
The ParameterCelFile class	ParameterCelFile
The ParameterCelSet class	ParameterCelSet
The ProbeAffinityFile class	ProbeAffinityFile
The ProbeLevelModel class	ProbeLevelModel
The ProbeLevelTransform class	ProbeLevelTransform
The ProbeLevelTransform3 class	ProbeLevelTransform3
The QualityAssessmentFile class	QualityAssessmentFile
The QualityAssessmentModel class	QualityAssessmentModel
The QualityAssessmentSet class	QualityAssessmentSet
The QuantileNormalization class	QuantileNormalization
The ReseqCrosstalkCalibration class	ReseqCrosstalkCalibration
The ResidualFile class	ResidualFile
The ResidualSet class	ResidualSet
The RmaBackgroundCorrection class	RmaBackgroundCorrection
The RmaCnPlm class	RmaCnPlm
The RmaPlm class	RmaPlm
The RmaSnpPlm class	RmaSnpPlm
The ScaleNormalization class	ScaleNormalization
The ScaleNormalization3 class	ScaleNormalization3
The SingleArrayUnitModel class	SingleArrayUnitModel
The SmoothMultiarrayModel class	SmoothMultiarrayModel
The SmoothRmaModel class	SmoothRmaModel
The SnpChipEffectFile class	SnpChipEffectFile
The SnpChipEffectSet class	SnpChipEffectSet
The SnpInformation class	SnpInformation
The SnpPlm interface class	SnpPlm
The SnpProbeAffinityFile class	SnpProbeAffinityFile
The SpatialReporter class	SpatialReporter
The TransformReport class	TransformReport
The UgpGenomeInformation class	UgpGenomeInformation
The UnitModel class	UnitModel
The UnitTypeScaleNormalization class	UnitTypeScaleNormalization
The WeightsFile class	WeightsFile
The WeightsSet class	WeightsSet

Package: aroma.affymetrix 3.2.2

aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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