affy

DOI: 10.18129/B9.bioc.affy  

This is the development version of affy; for the stable release version, see affy.

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Development (3.18)

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Author: Rafael A. Irizarry <rafa at ds.harvard.edu>, Laurent Gautier <lgautier at gmail.com>, Benjamin Milo Bolstad <bmb at bmbolstad.com>, and Crispin Miller <cmiller at picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand at astrazeneca.com>, Leslie M. Cope <cope at mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing at agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon at u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman at cbs.dtu.dk>, John Zhang

Maintainer: Rafael A. Irizarry <rafa at ds.harvard.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("affy")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, Software
Version	1.79.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	LGPL (>= 2.0)
Depends	R (>= 2.8.0), BiocGenerics(>= 0.1.12), Biobase(>= 2.5.5)
Imports	affyio(>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc
LinkingTo	preprocessCore
Suggests	tkWidgets(>= 1.19.0), affydata, widgetTools
SystemRequirements
Enhances
URL
Depends On Me	affyContam, affydata, affyPLM, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, bgx, bronchialIL13, ccTutorial, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, curatedOvarianData, DrugVsDisease, ecoliLeucine, ExiMiR, farms, frmaTools, gcrma, Hiiragi2013, logitT, maPredictDSC, MAQCsubset, maskBAD, mvoutData, panp, prebs, PREDAsampledata, qpcrNorm, RefPlus, Risa, RPA, SCAN.UPC, SpikeIn, SpikeInSubset, sscore, webbioc, XhybCasneuf
Imports Me	affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, crossmeta, DeSousa2013, Doscheda, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, rat2302frmavecs, rCGH, Rnits, signatureSearchData, STATegRa, tilingArray, TurboNorm, vsn
Suggests Me	AnnotationForge, ArrayExpress, arrays, autonomics, beadarray, beadarraySNP, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, factDesign, ffpeExampleData, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary	affy_1.79.0.zip
macOS Binary (x86_64)	affy_1.79.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/affy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/affy
Bioc Package Browser	https://code.bioconductor.org/browse/affy/
Package Short Url	https://bioconductor.org/packages/affy/
Package Downloads Report	Download Stats