affy pipeline

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 1.52.0
Stability Stable
Requirements BiocGenerics, Biobase
Maintained Yes



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  • person_outline Laurent Gautier <>

Publications for affy

affy citations

PMCID: 5778818

[…] was analyzed using genechip® human transcriptome array 2.0 microarrays (affymetrix; thermo fisher scientific, inc.) according to the manufacturer's protocol. the raw data were analyzed by using the affy package (version 1.55.0; affymetrix; thermo fisher scientific, inc.) in r (10). the robust multi-array average method was employed to corrects probe intensity values and the microarray data […]

PMCID: 5762305

[…] identify potential drug targets for ras. we firstly downloaded the gene microarray datasets with the accession number of gse37265 from geo and performed robust multi-array (rma) normalization with affy r programming package. secondly, differential expression genes (degs) in ras samples compared with control samples were identified based on limma package. enriched gene ontology (go) terms […]

PMCID: 5493306

[…] medical campus microarray and sequencing resource. cel files were normalized to produce gene-level expression values using the implementation of the robust multiarray average (rma) [32] in the affy package (version 1.36.1)[33] included within in the bioconductor software suite (version 2.11) and an entrez gene-specific probeset mapping (version 17.0.0) from the molecular and behavioral […]

PMCID: 5493619

[…] meta-analyses were conducted to increase the statistical significance and to minimize the noise intrinsic to gene expression measurements. microarray datasets were normalized using frma61 from the r affy package67. when multiple probes matched the same gene symbol, probes presenting the greatest inter-quartile range were selected. only genes present in all the selected platforms were considered […]

PMCID: 4913741

[…] and 14 osteosarcoma specimens, were available based on the affymetrix human genome u133a array., we converted the probe-level data in cel files into expression measures using the rma function of the affy package in r [14]. then, the r/bioconductor notes package of the microarray data platform was used to map probe sets to genes. for each sample, the expression values of all probes for a given […]

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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