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affy

Methods for Affymetrix Oligonucleotide Arrays


Bioconductor version: Release (3.19)

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")):

Installation

To install this package, start R (version "4.4") 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

Details

biocViews Microarray, OneChannel, Preprocessing, Software
Version 1.82.0
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 https://bioconductor.org/packages/affy
Bug Reports https://github.com/rafalab/affy/issues
See More
Suggests tkWidgets(>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Linking To preprocessCore
Enhances
Depends On Me affyContam, affyPLM, AffyRNADegradation, altcdfenvs, arrayMvout, bgx, Cormotif, DrugVsDisease, ExiMiR, frmaTools, gcrma, maskBAD, panp, prebs, qpcrNorm, RPA, SCAN.UPC, webbioc, affydata, ALLMLL, AmpAffyExample, bronchialIL13, CLL, curatedBladderData, ecoliLeucine, Hiiragi2013, MAQCsubset, mvoutData, PREDAsampledata, SpikeIn, SpikeInSubset, XhybCasneuf, RobLoxBioC
Imports Me affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bnem, CAFE, ChIPXpress, Cormotif, crossmeta, Doscheda, ffpe, frma, gcrma, GEOsubmission, Harshlight, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, Rnits, STATegRa, tilingArray, TurboNorm, vsn, rat2302frmavecs, DeSousa2013, signatureSearchData, bapred, seeker
Suggests Me AnnotationForge, ArrayExpress, autonomics, beadarray, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, factDesign, GeneRegionScan, limma, made4, piano, PREDA, qcmetrics, runibic, siggenes, TCGAbiolinks, ath1121501frmavecs, estrogen, ffpeExampleData, 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_1.82.0.tar.gz
Windows Binary affy_1.82.0.zip (64-bit only)
macOS Binary (x86_64) affy_1.82.0.tgz
macOS Binary (arm64) affy_1.82.0.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