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affy specifications


Unique identifier OMICS_00740
Name affy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.58.0
Stability Stable
methods, stats, graphics, utils, grDevices, zlibbioc, preprocessCore, R(>=2.8.0), BiocGenerics(>=0.1.12), Biobase(>=2.5.5), affyio(>=1.13.3), BiocInstaller, tkWidgets(>=1.19.0), affydata, widgetTools
Maintained Yes




No version available



  • person_outline Laurent Gautier

Publications for affy

affy citations


Modeling Transcriptional Rewiring in Neutrophils Through the Course of Treated Juvenile Idiopathic Arthritis

Sci Rep
PMCID: 5958082
PMID: 29773851
DOI: 10.1038/s41598-018-26163-4

[…] automated genechip™ 450 fluidics station and scanned with an affymetrix 3000 7 g scanner., to generate expression summary values from affymetrix exon and mirna arrays, rma software in the “affy” package of bioconductor in the r statistical computing environment ( was used with its default settings. for individual genes with multiple probe sets on the array […]


Expression profiling of cell intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages

PMCID: 5948821
PMID: 29751772
DOI: 10.1186/s13287-018-0848-7

[…] ( the raw intensity data were background corrected, log2 transformed and quantile normalized using the robust multi-array average (rma) algorithm implemented by the affy package []. the differentially expressed genes (degs) were further identified using the limma package []. the probe sets that demonstrated benjamini–hochberg adjusted p < 0.01 and log2 […]


Delineation of condition specific Cis and Trans acting elements in plant promoters under various Endo and exogenous stimuli

BMC Genomics
PMCID: 5954277
PMID: 29764390
DOI: 10.1186/s12864-018-4469-4

[…] ath1 microarray chip (gpl198). for all conditions, two replicate samples were analysed. array intensities were background adjusted and quantile normalized by using the justrma function in the affy package of bioconductor in r statistical language [, ]. the probe set annotation table downloaded from tair database (v10) was used to identify corresponding genes of each probe set ids []. […]


Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

Biotechnol Biofuels
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] using linear scaling to equilibrate the median values across the libraries. the pool of gene length- and library size-normalized values (fpkm) was additionally quantile-normalized via bioconductor “affy” package []. the differential expression testing was performed using ebseq [], the empirical bayesian-based differential expression calling package. genes with posterior probability […]


The dehydration stress of couch grass is associated with its lipid metabolism, the induction of transporters and the re programming of development coordinated by ABA

BMC Genomics
PMCID: 5930771
PMID: 29720087
DOI: 10.1186/s12864-018-4700-3

[…] within the r statistical package [] were used for the statistical analysis of the chip outputs. the microarray raw data were subjected to pre-processing analysis using functions provided with the affy package library [], with emphasis on boxplots, density plots and bland-altman plot modification (mva plot). subsequently, the rma method [] was implemented to achieve normalization […]


A remark on copy number variation detection methods

PLoS One
PMCID: 5922522
PMID: 29702671
DOI: 10.1371/journal.pone.0196226

[…] be applied in need instead of necessarily., data used for this study are available from the affymetrix snp (array data of 254 samples) at and released cnv reports at data are also from the hapmap project, 1000 genomes project and the vcf files and chrom 11 alignments of 128 samples […]

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affy institution(s)
Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Lyngby, Denmark; Department of Mathematical Sciences, Johns Hopkins University, Baltimore, MD, USA; Group in Biostatistics, University of California, Berkeley, CA, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
affy funding source(s)
This work was funded by the Danish Biotechnology Instrument Center and the Hopkins PGA Administrative and Bioinformatics Component (P01 HL 66583).

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