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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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Maintainer
- person_outline Laurent Gautier
Publications for affy
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
affy citations
(708)Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia Specific Potential Biomarkers
[…] 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 […]
The presence of human mesenchymal stem cells of renal origin in amniotic fluid increases with gestational time
[…] , 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 […]
SETDB2 Links E2A PBX1 to Cell Cycle Dysregulation in Acute Leukemia through CDKN2C Repression
[…] 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 […]
Micro RNA 186 5p inhibition attenuates proliferation, anchorage independent growth and invasion in metastatic prostate cancer cells
[…] 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). […]
Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma
[…] 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 […]
Framework for Parallel Preprocessing of Microarray Data Using Hadoop
[…] 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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