AgiMicroRna specifications

Information


Unique identifier OMICS_07859
Name AgiMicroRna
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
Requirements
limma, methods, gplots, Biobase, R(>=2.10), gtools, preprocessCore, marray, geneplotter, gdata, affy(>=1.22), affycoretools, codelink
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Pedro López-Romero <>

Publication for AgiMicroRna

AgiMicroRna in publications

 (41)
PMCID: 5777794
PMID: 29383182
DOI: 10.18632/oncotarget.23311

[…] with a small number of replicates []. differential expression was defined for genes with fdr < 0.05., mirna expression was profiled by agilent microarrays, and processed and normalized using the agimicrorna r package (using between-array quantile normalization) []. to filter mirnas with very low expression across most epn samples, we removed mirnas that were detected in < 25% of samples […]

PMCID: 5595893
PMID: 28900269
DOI: 10.1038/s41598-017-11638-7

[…] id, refseq mrna, and genbank accession numbers. mir expression signals were extracted from microarray images using agilent feature extraction (fe) software, and normalized using either lvsmirna or agimicrorna package from bioconductor. these normalization methods were used based on literature suggesting distinct advantages offered by each in normalizing gene expression data–. lvsmirna uses […]

PMCID: 5591958
PMID: 28928672
DOI: 10.3389/fphys.2017.00648

[…] (deposited at gene expression omnibus under geo series accession number gse101616) were normalized using the robust multi-array average (rma) method (irizarry et al., ) implemented in the agimicrorna bioconductor package, and the fold changes in circulating mirnas were determined using the linear model implemented in the limma bioconductor package (ritchie et al., ). the benjamini […]

PMCID: 5476258
PMID: 28628672
DOI: 10.1371/journal.pone.0179583

[…] data, a detection p-value was used to filter out non-expressed mirna leading to consider 325 (differentiation) or 483 probes (bps) as expressed. the normalization was performed with the r package agimicrorna []., for each one of the product (bpa, bpf, bps), 12 assays of cell cultures differentiated without any product (negative control, 4 per patient), 12 assays of cell cultures […]

PMCID: 5472579
PMID: 28620241
DOI: 10.1038/s41598-017-03456-8

[…] sure scan high-resolution technology (agilent technologies). the images were analyzed and quantified with the agilent feature extraction software (afe version 11.5). the r/bioconductor softwares agimicrorna and limma packages were used to perform the normalization and statistical analysis of the extracted data. for microrna arrays, the afe signal used was totalgenesignal (the sum […]


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AgiMicroRna institution(s)
Epidemiology, Atherothrombosis and Imaging Department Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Melchor Fernández Almagro, Madrid, Spain

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