affy

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

Methods for Affymetrix Oligonucleotide Arrays

Bioconductor version: Development (3.24)

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.dfci.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: Robert D. Shear <rshear at ds.dfci.harvard.edu>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.91.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21 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
System Requirements
URL	https://bioconductor.org/packages/affy
Bug Reports	https://github.com/rafalab/affy/issues

Suggests	tkWidgets(>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Linking To	preprocessCore
Enhances
Depends On Me	affyContam, affyPLM, AffyRNADegradation, altcdfenvs, arrayMvout, Cormotif, DrugVsDisease, ExiMiR, frmaTools, gcrma, maskBAD, panp, prebs, qpcrNorm, RPA, SCAN.UPC, webbioc, affydata, ALLMLL, AmpAffyExample, bronchialIL13, CLL, curatedBladderData, ecoliLeucine, MAQCsubset, mvoutData, PREDAsampledata, SpikeIn, SpikeInSubset, XhybCasneuf
Imports Me	affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, Doscheda, ffpe, frma, gcrma, GEOsubmission, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, Rnits, STATegRa, tilingArray, TurboNorm, vsn, rat2302frmavecs, DeSousa2013, signatureSearchData, bapred
Suggests Me	AnnotationForge, ArrayExpress, autonomics, beadarray, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, factDesign, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks, ath1121501frmavecs, estrogen, ffpeExampleData, Hiiragi2013, arrays, aroma.affymetrix, hexbin, isatabr, maGUI
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	affy_1.91.0.tar.gz
Windows Binary (x86_64)	affy_1.91.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	affy_1.91.0.tgz
macOS Binary (sonoma-arm64)	affy_1.91.0.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