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Tool usage distribution map

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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 1.58.0
Stability Stable
Requirements
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

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Versioning


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Documentation


Maintainer


  • person_outline Laurent Gautier

Publications for affy

affy citations

 (708)
library_books

Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia Specific Potential Biomarkers

2018
PMCID: 5932158
PMID: 29755398
DOI: 10.3389/fneur.2018.00266

[…] rain cell types and differential expression of induced pluripotent stem cells (iPSCs) versus derived microglia. This data series deposited in GEO database contains human microglia-specific microarray Affy HuGene-2_0-st data (GSE78115) (). Specifically, we considered the 12 samples (3 replicates each) derived from 2 different cell lines NCRM-5 and iNC-01 of iPSC origin. Using OLIGO package of R Bio […]

call_split

The presence of human mesenchymal stem cells of renal origin in amniotic fluid increases with gestational time

2018
PMCID: 5918774
PMID: 29695308
DOI: 10.1186/s13287-018-0864-7
call_split See protocol

[…] , Düsseldorf, Germany). The gene expression profile for AF-MSCs, HREpCs, fMSCs, UM51 and ISRM-UM51 are provided online at the National Center of Biotechnology Information Gene Expression Omnibus. The affy package of the R/Bioconductor environment [, ] was used for further processing of the unnormalized bead summary data. After background correction, the data were transformed to a logarithmic scale […]

library_books

SETDB2 Links E2A PBX1 to Cell Cycle Dysregulation in Acute Leukemia through CDKN2C Repression

2018
Cell Rep
PMCID: 5963704
PMID: 29694893
DOI: 10.1016/j.celrep.2018.03.124

[…] ap.2. Primary leukemia expression microarrays were accessed from GEO: GSE13204 (). Raw microarray image processing, expression calling, and normalization were performed by the R-Bioconductor package “affy.” ChIP-seq samples were analyzed as follows: (1) Reads mapped by BWA to human genome assembly hg19; (2) peaks were called and differential peaks were analyzed using MAC2; (3) peaks were viewed by […]

library_books

Micro RNA 186 5p inhibition attenuates proliferation, anchorage independent growth and invasion in metastatic prostate cancer cells

2018
BMC Cancer
PMCID: 5899400
PMID: 29653561
DOI: 10.1186/s12885-018-4258-0

[…] a, CA), according to the manufacturer’s instructions. Each array was washed and stained according to array type. The fluidics protocol FS450_0002 was used to analyze each array via Gene chip scanner (Affy.Command console Version 3.3). […]

call_split

Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma

2018
Sci Rep
PMCID: 5882888
PMID: 29615643
DOI: 10.1038/s41598-018-23609-7
call_split See protocol

[…] ients with sporadic VS, 16 patients with NF2 syndrome-associated VS, and 7 control nerves were generously donated by Agnihotri et al.. CEL files were loaded into R using the justRMA function from the affy package in R. justRMA is an automated tool that both performs normalization using the Robust Multi-Array Average method and also automatically annotates all probes in the normalized dataset using […]

library_books

Framework for Parallel Preprocessing of Microarray Data Using Hadoop

2018
Adv Bioinformatics
PMCID: 5896349
DOI: 10.1155/2018/9391635

[…] HDFS. Then it runs the preprocessing method in the model of MapReduce programing to propagate the jobs and tasks across all nodes. Consequently, preprocessing performance of microarray data increases.Affy-library and RHadoop framework make Hadoop HDFS accessible. The  .CEL files along with  .cdf files (chip description file) which are uploaded from local machines are placed into HDFS which is loca […]


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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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