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Preprocessing tools for oligonucleotide arrays

Bioconductor version: Release (3.19)

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Author: Benilton Carvalho and Rafael Irizarry

Maintainer: Benilton Carvalho <benilton at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

oligo User's Guide PDF
Reference Manual PDF


biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel
Version 1.68.2
In Bioconductor since BioC 2.0 (R-2.5) (17 years)
License LGPL (>= 2)
Depends R (>= 3.2.0), BiocGenerics(>= 0.13.11), oligoClasses(>= 1.29.6), Biobase(>= 2.27.3), Biostrings(>= 2.35.12)
Imports affyio(>= 1.35.0), affxparser(>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore(>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc
System Requirements
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Suggests BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240,, pd.hg18.60mer.expr,, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl
Linking To preprocessCore
Enhances doMC, doMPI
Depends On Me ITALICS, pdInfoBuilder, puma, SCAN.UPC, oligoData, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter,,,, pd.ath1.121501, pd.barley1,,, pd.bovine, pd.bsubtilis,,, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken,,,,, pd.citrus, pd.clariom.d.human, pd.clariom.s.human,, pd.clariom.s.mouse,, pd.clariom.s.rat,, pd.cotton,,,,, pd.cytogenetics.array,,, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2,,,,,,,,,,, pd.genomewidesnp.5, pd.genomewidesnp.6,,, pd.hc.g110, pd.hg.focus,, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr,,,, pd.hta.2.0, pd.hu6800,,,,,, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240,,,,, pd.medicago,,,,,,, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, pd.mirna.4.0, pd.moe430a, pd.moe430b,,,,,, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177,,, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine,,,,, pd.rae230a, pd.rae230b,,,,,, pd.rat230.2,,, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c,,, pd.rhesus, pd.rice,,, pd.rn.u34, pd.rta.1.0,,, pd.s.aureus, pd.soybean,,, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98,,, pd.zebrafish, pd.atdschip.tiling, pumadata, maEndToEnd
Imports Me ArrayExpress, cn.farms, crossmeta, frma, ITALICS, mimager
Suggests Me fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex, aroma.affymetrix, maGUI, RCPA
Links To Me
Build Report Build Report

Package Archives

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

Source Package oligo_1.68.2.tar.gz
Windows Binary
macOS Binary (x86_64) oligo_1.68.2.tgz
macOS Binary (arm64) oligo_1.68.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive