affy

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see affy.

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: 3.11

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 jhu.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 jhu.edu>

Citation (from within R, enter citation("affy")):

Installation

To install this package, start R (version "4.0") and enter:


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

BiocManager::install("affy")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("affy")

1. Primer	PDF	R Script
2. Built-in Processing Methods	PDF	R Script
3. Custom Processing Methods	PDF	R Script
4. Import Methods	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, OneChannel, Preprocessing, Software
Version	1.66.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19 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
System Requirements
URL

Suggests	tkWidgets(>= 1.19.0), affydata, widgetTools
Linking To	preprocessCore
Enhances
Depends On Me	affyContam, affydata, AffyExpress, affyPara, affypdnn, affyPLM, affyQCReport, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, ArrayTools, bgx, bronchialIL13, ccTutorial, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, curatedOvarianData, DrugVsDisease, dualKS, ecoliLeucine, ExiMiR, farms, frmaTools, gcrma, Hiiragi2013, LMGene, logitT, maPredictDSC, MAQCsubset, MAQCsubsetAFX, maskBAD, MLP, mvoutData, panp, plw, prebs, PREDAsampledata, qpcrNorm, RefPlus, Risa, RPA, SCAN.UPC, simpleaffy, SpikeIn, SpikeInSubset, sscore, Starr, webbioc, XhybCasneuf
Imports Me	affycoretools, affyILM, affylmGUI, affyQCReport, arrayQualityMetrics, ArrayTools, CAFE, ChIPXpress, coexnet, Cormotif, crossmeta, DeSousa2013, Doscheda, EGAD, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, iCheck, lumi, LVSmiRNA, makecdfenv, mimager, MSnbase, PECA, plier, plw, puma, pvac, rat2302frmavecs, rCGH, Rnits, signatureSearchData, simpleaffy, STATegRa, tilingArray, TurboNorm, vsn, waveTiling
Suggests Me	AnnotationForge, ArrayExpress, arrays, beadarray, beadarraySNP, BiocCaseStudies, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, ExpressionView, factDesign, ffpeExampleData, gCMAPWeb, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	affy_1.66.0.tar.gz
Windows Binary	affy_1.66.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	affy_1.66.0.tgz
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
Old Source Packages for BioC 3.11	Source Archive