aroma.affymetrix

3.2.3

Analysis of Large Affymetrix Microarray Data Sets

1packages depend

9.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Henrik BengtssonFirst published 2009-06-2946 releasesCRAN page ↗GitHub ↗

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("aroma.affymetrix", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("HenrikBengtsson/aroma.affymetrix")

Development version from HenrikBengtsson/aroma.affymetrix. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-aroma.affymetrix

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 8.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

OK2026-06-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 14%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 5%

Downloads

9.3K

CRAN downloads in the past year

Rank #5,133 · ~25/day · ~775/mo

Releases R versions

Daily download trend is not available in this view yet.

58330 days

1.8K90 days

9.3K1 year

Compare downloads with other packages →

Also on270 r2u1.6K bioconda

Repository

GitHub ↗ henrikbengtsson/aroma.affymetrix

12Stars

3Forks

8Open issues

0Open PRs

0Releases

911Commits

4Contributors

rpackageaffymetrixcopy-numberexpressiondnarnaanalysis

911 commits · Last activity 2025-12-14 · 0% stars, 30d

Stars over time

2025-07-08 · 112026-07-07 · 12

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/henrikbengtsson/aroma.affymetrix on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdrevdep/

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.2.0R.utils aroma.core

Imports (12)

methodsR.methodsS3 R.oo R.cache (>= 0.14.0)R.devices R.filesets aroma.apdMASSsplinesmatrixStats listenv future

LinkingTo (0)

none

Suggests (16)

DBI RColorBrewer Biobase BiocGenerics affxparser affy (>= 1.46.0)affyPLM aroma.light gcrma (>= 2.40.0)limma oligo oligoClasses (>= 1.30.0)pdInfoBuilder preprocessCore AffymetrixDataTestFiles dChipIO

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

ACNE

Code & Tests

People & History

People (7)

Maintainer (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Authors (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Contributors (6)

James Bullard

Contributor · added in 2.14.2

Kasper Hansen

Contributor · added in 2.14.2

Pierre Neuvial

Contributor · added in 1.7.0

Contributor

Contributor

Contributor

Author, Maintainer, Copyright holder

Package Timeline

46 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
3.2.3Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
3.2.2
2024-02-18 · diff ↗
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R 4.3.0 released · 2023-04-21
3.2.1
2022-07-18 · diff ↗
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R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
3.2.0
2019-06-23 · diff ↗
R
R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
3.1.1
2018-04-16 · diff ↗
R
R 3.4.0 released · 2017-04-21
3.1.0
2017-03-24 · diff ↗

Show 51 earlier events

R
R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
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R 3.0.0 released · 2013-04-03
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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2011-08-29 · diff ↗
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R 2.13.0 released · 2011-04-13
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R
R 2.12.0 released · 2010-10-15
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2010-05-16 · diff ↗
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R 2.11.0 released · 2010-04-22
1.5.0
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2.11.0
2010-02-22 · diff ↗
1.4.0
2010-01-07 · diff ↗
1.3.0
2009-11-03 · diff ↗
2.10.1
2009-11-01 · diff ↗
R
R 2.10.0 released · 2009-10-26
1.2.0
2009-09-10 · diff ↗
2.9.2
2009-06-29 · diff ↗
1.1.1
2009-06-29
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-06-29
Total releases: 46 / 17 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.2.0
Download size: 735 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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