affy protocols

affy specifications

Information


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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Maintainer


  • person_outline Laurent Gautier <>

Publications for affy

affy IN pipelines

 (17)
2017
PMCID: 5493306
PMID: 28665939
DOI: 10.1371/journal.pone.0179797

[…] 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 […]

2017
PMCID: 5493619
PMID: 28667284
DOI: 10.1038/s41598-017-04400-6

[…] 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 […]

2017
PMCID: 5556079
PMID: 28808310
DOI: 10.1038/s41598-017-08615-5

[…] of patients used in this study was shown in table 2., raw microarray data files (.cel files) of the three datasets were analyzed using the robust multichip average (rma) algorithm by the r package affy36. after that, the linear models for microarray data (limma) package in r was used to calculate the probability of probes being differentially expressed between cases and controls37. p value […]

2017
PMCID: 5762305
PMID: 29340037
DOI: 10.18632/oncotarget.22347

[…] 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 […]

2017
PMCID: 5778818
PMID: 29435009
DOI: 10.3892/ol.2017.7691

[…] 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 […]

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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